So, your basic set of steps is:

1. Read file1
2. Read file2
3. Write file3 with each line from file1 and file2

What happens if they don't have the same number of lines?

chomp( my @file1 = do { open FH, (+shift); <FH> } );
chomp( my @file2 = do { open FH, (+shift); <FH> } );

my @file3;
while( @file1 && @file2)
{
    push @file3, join(' ', shift(@file1), shift(@file2));
}

open FH, ">output";
print FH join($/, @file3, '');
close FH;
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Of course, you're going to want to add some error-handling for the file operations.