while (my $line = <MYFILE>)
{
   chomp $line;

   # Do stuff here
}

##</code><code>##

while (<MYFILE>)
{
    # Skip commented-out lines (or whatever else you want to do)
    next if /^#/; 

    # Don't chomp unless we know we're going to use the line
    chomp;

    if (/SOME REGEX HERE/)
    {
        # Do stuff
    }
}