I use a belt sander with 80 grit paper, and a slow speed and a light touch.  The soft copper wire ends are easily sanded off without harm to the plywood.

You can also buy a cheap pair of small side cutters and grind down the closed face a bit to take away the inner bevel of the cutting face (see photo).  This will allow the face to sit tight against the hull and you can snip the wire flush.  As Ron mentioned, any small nubs will then easily sand down to nothing.

Chris

This is why I pull the wires, rather than leave them in. The easiest way is to tack glue the joints and remove the wire before putting in the fillets. If they're already bedded in epoxy putty, then a slow firm pull with combination pliers almost always works for me. When it doesn't, a quick touch with a soldering iron will heat the wire enough to locally and temporarily soften the epoxy enough to let the wire be pulled.

Laszlo 

A pair of nail clippers works well for cutting narrow gauge wire and typically leaves a clean square edge.

Scott

Don't make the mistake I made and heat the copper ends with a candle.  Scorch marks don;t come off.  This is one reason my Wood Duck is painted. 

You don't want to use a rasp.

Your worries are unwarranted. Some wire is not a problem. I got out 99% of mine, some remained. When you sand the boat, they will sand away and you won't even know you are sanding the wire. Copper is very soft.

To minimize metal and cut as close as you can, don't use a regular cutter, use what is called a 'flush cutter'. They work great. I didn't use one, didn't have one on hand, not a problem.

Don't worry about getting it close to the wood at all.  I used my ROS, and it easily ground through the copper like it wasn't there.  I don't think I used more than a couple of pieces of sandpaper to sand away all of the wire.

Make sure you hold the sander flat so it doesn't gouge where you are removing the wire, but as a reference point, I think dried epoxy is more difficult to remove than copper wire.