How do I pull up sheets of plywood from the floor?
You should be able to pull them up with a 12" long prybar and possibly a crowbar (3' to 4' long), if it is stubborn.  Most that I have seen are put in with nails only.  You may also need to have a circular saw handy in case some of the subfloor runs underneath a wall (in this case, you would want to make a clean cut of the subfloor piece, so you can remove the part that you need and leave the part under the wall intact).

As for reattaching the sheets, you should use 3" screws.