Howdy cniggeler, welcome to the Monastery!

When you pipe data into a script, its STDIN is connected to that pipe, so if you want to read from the console again, you'll have to close and reopen STDIN:

#!/usr/bin/perl

use strict;
use warnings;
use feature qw/say/;

chomp(my @filelist = <STDIN>);

close STDIN;
open STDIN, "<", "/dev/tty" or die "Cannot reopen STDIN";

foreach(@filelist) {
    print "Do you wish to modify $_? (y/n) ";
    my $ans = uc <STDIN>;
    say "$_ modified" if $ans =~ m/^Y/;
}
[download]

(There may well be CPAN modules for this sort of thing, too; I haven't checked.)