Jonathan ( @JonathanH ) and I have been trading messages about fly boxes and I needed to post some pictures to better explain myself. So I thought I'd move that whole discussion here just in case someone else is interested and more important, in case someone else has a better idea.
Wooden fly boxes are not commonly carried while fishing although they certainly could be. Most of time, a fancy wood fly box is used to save and display special flies, sometimes flies that caught a "life" fish; flies tied by someone special; flies tied by the owner but ones he or she wants to save. Obviously wood fly boxes make special gifts for a fly fisherman. Not to be exclusionary, you could easily apply the same description to a box that was made for hardware lures instead of flies. Most boxes of this nature have relatively thin sides, top and bottom because weight is a concern in fly boxes. Since this box isn't going to be carried around weight isn't such a big deal but we still like to make the box with thin sides, smallest hinges we can find, etc. We were talking about methods for making a fly box and I was trying to explain the router method I used. So here's where we'll start.
The router method is pretty fool proof because you use a pattern. The collar of the router follows along the inside edge of whatever pattern you design and as long as you keep the router base flat on your pattern, it cannot go anywhere you don't want it to go.
1. Pattern: your pattern board needs to be cut from wood that is just slightly thicker than the collars you have for your router. I could be wrong but I think most pattern collars for routers today are around 3/16" to 1/4". I used a scrap piece of 5/16" plywood for this pattern. You also need to consider how you will secure the pattern to your work bench while routing. I clamp mine using trigger clamps. So that means I need to have enough overhang on my pattern for the clamps AND also to allow my router base full access around the pattern. For demonstration purposes, I'll photograph my pattern for a 4"x4" fly box. The total pattern board is at least 24" long with the pattern cut in the middle.
I found it helpful for me to glue in strips of wood to frame the wood that will be routed. In this case, I used some scrap 3/8" pine. Glue the scrap pieces so the inside dimension fits the blanks you'll be using. In this case it's 4"x4", but you could make it 4"x6" or whatever. These scraps secure the actual wood and prevent it from sliding around under the pattern as the vibration from the router gets going. Notice that the cutout for the pattern is around 1/8" smaller than the outer dimension of the fly box. You can adjust this to achieve whatever thickness you desire for the walls of your fly box (remember you can always trim it later or sand it down if it's just evening up the edges, etc). Trying to get much thinner though you increase the risk of blowout from the router bit, so I recommend 1/8" or slightly thicker. You can always sand the finished box to get thinner sides if you want. If you don't want to install these positioning scrap pieces, you can use a couple strips of double stick tape to help hold the blank in place while you route it. In this close up shot, you can see the positioning scraps are glued in place leaving a 1/8" reveal (that will be the thickness of the sides of the finished box). And the scrap pieces are glued in to snugly secure the 4"x4" block of wood that I want to use for the fly box.
Note: it's better to use a larger blank and cut it to final shape after routing the inside than to try shim in a blank that's slightly too small for your pattern. Or remake your pattern slightly smaller to fit the blank you're using.
One other point, this pattern is for one side of the fly box. I'll have to duplicate this process twice and route two blanks to make a complete box. You could make a double pattern that allows you to route both sides of the fly box without having to unclamp and install a second piece of wood. If you have a long board and want to route the inside of the fly box and then cut it apart with a band saw or on the table saw, that would be the way to go. Just duplicate the cutout you see above (so there are two cutouts in your pattern. Position it on the board you want to make the fly box from, clamp it in place and route the inside. Then remove the pattern and cut the boxes apart on your saw. This might allow even thinner sides if you want. Note: you can use a single pattern also, you'll just have to route one side, and then reposition the pattern on your board to route the other side, and then cut the sides apart on your band saw. Note: if you're doing this, don't glue scraps of wood to frame your blank, just leave your pattern board flat and use double stick tape to help secure it to the blank.
2. Pattern shape: your pattern needs to accommodate whatever hinges you plan to use and if you plan to use tiny magnets to close the box. I get the smallest brass coated hinges from Lowes or Home Depot, but you can probably find small hinges from specialty suppliers too. Generally, the sides of the finished box are too narrow to screw hinges to, so I leave wider areas where the hinges will go. For my boxes I locate those wider areas in the rear corners. That leaves more of the space inside the box for flies. Nothing says you couldn't move the hinges inward but that makes for a more complicated pattern and small narrow spaces between the hinge and side of the box, etc. And I like using tiny magnets for closures so on the side of the pattern opposite the hinges, you see a small bump. When routed, this will leave a wider area into which I'll drill a hole and glue in the magnet. If you are using an external clasp or something, you can omit this "bump' in your pattern.
3. Routing: test fit the blanks you will be routing. They should fit snugly inside the scrap pieces you glued around the pattern cutout. You can see this gamble oak blank I'm trading to Jonathan is too small for my existing pattern and I'd have to remake the pattern if I were to use these gamble oak blanks.
If your happy with the fit of your blank, flip the whole thing over and clamp it to your work bench. I use two trigger clamps with 3/8" scrap pieces under the overhangs to get a solid clamp pressure. I've also found it helpful if I have a piece of sand paper taped down on my bench under the blank, it helps prevent the whole thing from vibrating and moving around. I use a 3/8" three flute down cut bit (down cut because it leaves a cleaner edge along the inside of the box), but an up cut bit probably works just as well and helps throw the chips out of the cutout. I set my router depth so the initial pass is about 1/8" deep. Start the cut with the bit slightly inside the edge of your pattern and slide the router over until the collar is up against your pattern. Then going clockwise, make a smooth pass around the pattern. Once you've gone all the way around your pattern, start routing out the rest of the inside. I go back and forth trying to just overlap the bit width. It isn't crucial you do this neatly, but if you overlap too much, you'll leave little nubs you have to go back and route away. Once you've completely cleaned out this first pass inside your pattern, lower your bit another 1/8" more or less, and repeat. Keep doing this until you get to the desired final thickness of the bottom of your box. When you've reached that point, I lower my bit a fraction and make one final pass to clean up the cuts as much as I can to minimize sanding. And you have one side of your fly box ready to sand. Test fit the other blank, flip it over, clamp it in place and route the second side of your box in the same manner.
Note: if you are trying to align or match grain, make sure you check how you've positioned your blank in the pattern board before you start routing.
Wooden fly boxes are not commonly carried while fishing although they certainly could be. Most of time, a fancy wood fly box is used to save and display special flies, sometimes flies that caught a "life" fish; flies tied by someone special; flies tied by the owner but ones he or she wants to save. Obviously wood fly boxes make special gifts for a fly fisherman. Not to be exclusionary, you could easily apply the same description to a box that was made for hardware lures instead of flies. Most boxes of this nature have relatively thin sides, top and bottom because weight is a concern in fly boxes. Since this box isn't going to be carried around weight isn't such a big deal but we still like to make the box with thin sides, smallest hinges we can find, etc. We were talking about methods for making a fly box and I was trying to explain the router method I used. So here's where we'll start.
The router method is pretty fool proof because you use a pattern. The collar of the router follows along the inside edge of whatever pattern you design and as long as you keep the router base flat on your pattern, it cannot go anywhere you don't want it to go.
1. Pattern: your pattern board needs to be cut from wood that is just slightly thicker than the collars you have for your router. I could be wrong but I think most pattern collars for routers today are around 3/16" to 1/4". I used a scrap piece of 5/16" plywood for this pattern. You also need to consider how you will secure the pattern to your work bench while routing. I clamp mine using trigger clamps. So that means I need to have enough overhang on my pattern for the clamps AND also to allow my router base full access around the pattern. For demonstration purposes, I'll photograph my pattern for a 4"x4" fly box. The total pattern board is at least 24" long with the pattern cut in the middle.

I found it helpful for me to glue in strips of wood to frame the wood that will be routed. In this case, I used some scrap 3/8" pine. Glue the scrap pieces so the inside dimension fits the blanks you'll be using. In this case it's 4"x4", but you could make it 4"x6" or whatever. These scraps secure the actual wood and prevent it from sliding around under the pattern as the vibration from the router gets going. Notice that the cutout for the pattern is around 1/8" smaller than the outer dimension of the fly box. You can adjust this to achieve whatever thickness you desire for the walls of your fly box (remember you can always trim it later or sand it down if it's just evening up the edges, etc). Trying to get much thinner though you increase the risk of blowout from the router bit, so I recommend 1/8" or slightly thicker. You can always sand the finished box to get thinner sides if you want. If you don't want to install these positioning scrap pieces, you can use a couple strips of double stick tape to help hold the blank in place while you route it. In this close up shot, you can see the positioning scraps are glued in place leaving a 1/8" reveal (that will be the thickness of the sides of the finished box). And the scrap pieces are glued in to snugly secure the 4"x4" block of wood that I want to use for the fly box.

Note: it's better to use a larger blank and cut it to final shape after routing the inside than to try shim in a blank that's slightly too small for your pattern. Or remake your pattern slightly smaller to fit the blank you're using.
One other point, this pattern is for one side of the fly box. I'll have to duplicate this process twice and route two blanks to make a complete box. You could make a double pattern that allows you to route both sides of the fly box without having to unclamp and install a second piece of wood. If you have a long board and want to route the inside of the fly box and then cut it apart with a band saw or on the table saw, that would be the way to go. Just duplicate the cutout you see above (so there are two cutouts in your pattern. Position it on the board you want to make the fly box from, clamp it in place and route the inside. Then remove the pattern and cut the boxes apart on your saw. This might allow even thinner sides if you want. Note: you can use a single pattern also, you'll just have to route one side, and then reposition the pattern on your board to route the other side, and then cut the sides apart on your band saw. Note: if you're doing this, don't glue scraps of wood to frame your blank, just leave your pattern board flat and use double stick tape to help secure it to the blank.
2. Pattern shape: your pattern needs to accommodate whatever hinges you plan to use and if you plan to use tiny magnets to close the box. I get the smallest brass coated hinges from Lowes or Home Depot, but you can probably find small hinges from specialty suppliers too. Generally, the sides of the finished box are too narrow to screw hinges to, so I leave wider areas where the hinges will go. For my boxes I locate those wider areas in the rear corners. That leaves more of the space inside the box for flies. Nothing says you couldn't move the hinges inward but that makes for a more complicated pattern and small narrow spaces between the hinge and side of the box, etc. And I like using tiny magnets for closures so on the side of the pattern opposite the hinges, you see a small bump. When routed, this will leave a wider area into which I'll drill a hole and glue in the magnet. If you are using an external clasp or something, you can omit this "bump' in your pattern.
3. Routing: test fit the blanks you will be routing. They should fit snugly inside the scrap pieces you glued around the pattern cutout. You can see this gamble oak blank I'm trading to Jonathan is too small for my existing pattern and I'd have to remake the pattern if I were to use these gamble oak blanks.

If your happy with the fit of your blank, flip the whole thing over and clamp it to your work bench. I use two trigger clamps with 3/8" scrap pieces under the overhangs to get a solid clamp pressure. I've also found it helpful if I have a piece of sand paper taped down on my bench under the blank, it helps prevent the whole thing from vibrating and moving around. I use a 3/8" three flute down cut bit (down cut because it leaves a cleaner edge along the inside of the box), but an up cut bit probably works just as well and helps throw the chips out of the cutout. I set my router depth so the initial pass is about 1/8" deep. Start the cut with the bit slightly inside the edge of your pattern and slide the router over until the collar is up against your pattern. Then going clockwise, make a smooth pass around the pattern. Once you've gone all the way around your pattern, start routing out the rest of the inside. I go back and forth trying to just overlap the bit width. It isn't crucial you do this neatly, but if you overlap too much, you'll leave little nubs you have to go back and route away. Once you've completely cleaned out this first pass inside your pattern, lower your bit another 1/8" more or less, and repeat. Keep doing this until you get to the desired final thickness of the bottom of your box. When you've reached that point, I lower my bit a fraction and make one final pass to clean up the cuts as much as I can to minimize sanding. And you have one side of your fly box ready to sand. Test fit the other blank, flip it over, clamp it in place and route the second side of your box in the same manner.
Note: if you are trying to align or match grain, make sure you check how you've positioned your blank in the pattern board before you start routing.

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