I love extracting the maps and printing them up full color... The only problem comes when "secret" or "trap" markings aren't in separate layers. Then you either need to edit them pixel by pixel before printing, or ask your players to pretend that they can't see the red marks...
I usually do a bit of copy and paste from another part of the map to remove the secret doors and rooms (sometimes put a logo on the covered room so that players don't realize that there is a blank space and metagame).
I print up the map a second time with the secret doors and rooms indicated, cut them out, laminate and simply drop them in place when/if they are found.