If you're trying to alter file1 to be the set complement of the two files, you could use this to do it on the fly and not create a temp file: 
use Tie::File;

my %seen;
tie my @file1, 'Tie::File', 'file1' or die;
tie my @file2, 'Tie::File', 'file2' or die;

foreach (@file2) { chomp; $seen{$_}++; }
@file1 = grep { chomp; !$seen{$_} } @file1;

untie(@file1);
untie(@file2);

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In reply to Re: compare two files by wojtyk
in thread compare two files by Anonymous Monk

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