@all_patterns = (s/#.*//, s/^\s+//, s/\s+$//, s/^Total//, s/^,// );
# and so on

while(<FILE1>) {
 apply_patterns($_, (0,2,3)); # apply patterns 0, 2 and 3
}

while(<FILE2>) {
 apply_patterns($_, (2,5,7)); # apply patterns 2, 5 and 7
}

while(<FILE3>) {
 apply_patterns($_, (5,4,3)); # apply patterns 5, 4 and 3
}