It's almost certainly a scoping problem, as others have said.

Additionally, I'm not sure what you're trying to do in this Wanted. Even if you had proper scoping, you'd still be re-assigning the variable each time you went over it - in the end, you'd just have whatever the last value that matched the test.

Here's a try at something more reasonable:

my @foundfiles;
sub Wanted {
   return unless (-f $_);
   # only operate on compiled widgets
    /\.wgt$/ or return;

    my $file = $_;

    chomp ($file);
    chomp ($line);
    #print $file ." \n" if $file eq $line;
    if (lc($line) eq lc($file)){
        # Adds the files to the array
        push @foundFiles, $File::Find::name;
    }
    return;
}
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Alternately, you could keep foundfile as a scalar, and append to it thusly:

Either way, the important thing is that your variable needs to be in a scope where it won't go away before you use it.

These are pretty common errors, and Perl can catch a lot of them. If you aren't already, start putting this code at the top of every Perl program you write:

use strict;
use warnings;
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This will catch a LOT of problems before they turn into headaches. For even more detail (at some performance cost, you can use diagnostics;