Immediate thoughts:

• use strict;Always
• &MarkClose; should become &MarkClose();
• The if (@InFileNames > 0){ is redundant. Just have the foreach execute 0 times
• s/<div type=[^>]* id="([^>]*)">/$1/gms since a space is not a > the [^>]* will gobble a lot more string than I think you expect. Try [^>\s]*
• Use the debugger (perl -d) and try things one line at a time
• K&R indentation :-(

Update: OK once more but this time with real square brackets