There's not a lot to do to be fair, I need to remove the extension because I have files with the same name but different extensions. I'm trying to read them in and compare the different files. So I thought if I remove the extension in the array I can do something like this

#! /usr/bin/perl -w

my @files= <*.in>

for (@files)
{
    remove extension 
}

for my $file (@files)
{
    open (IN, "<", "$file.fo") || die ("cannot open $file.fo");
    open (OUT,"<", "$file.bo") || die ("cannot open $file.bo");

    undef $/;

    my $in = <IN>;
    my $out = <OUT>;
    my @in = split /\n/, $in;
    my @out = split /\n/, $out;
    my @final;

    for $a (@in)
    {
        my @result = grep/^\Q$a\E$/, @out;
        push (@final , @result);
    }

    print "Search string that matches against general data:\t@final";
}
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