I am really having trouble making any sense of your code.

I started by re-organizing your first statements with spacing
and some print statements:

use strict;
use warnings;

my $footprint_im = 'jpg gif png tiff tif';
$footprint_im .= ' '.uc $footprint_im;
$footprint_im =~ s/ /\$\|/g;
print "footprint_im = $footprint_im\n\n";
# footprint_im = jpg$|gif$|png$|tiff$|tif$|JPG$|GIF$|PNG$|TIFF$|TIF

my $footprint_iv = '^vid.+ 3gp mp4 avi';
$footprint_iv .= ' '.uc $footprint_iv;
$footprint_iv =~ s/ /\$\|/g;
print "footprint_iv = $footprint_iv\n\n";
# footprint_iv = ^vid.+$|3gp$|mp4$|avi$|^VID.+$|3GP$|MP4$|AVI

my $footprint_lnk = 'lnk';
$footprint_lnk .= ' '.uc $footprint_lnk;
$footprint_lnk =~ s/ /\$\|/g;
print "footprint_lnk = $footprint_lnk\n\n";
# footprint_lnk = lnk$|LNK
[download]

I am very confused about where @input comes from?

A statement like this: for($i = 1 ; $i <= @ff ;$i++){} means to iterate to the number of elements in the ff array. WHAT?

Perhaps start by explaining what you are trying to do. Then get some code to compile with use warnings; use strict;

Update: Perhaps:

my @image_files = grep{/\.jpg$|\.gif$|\.tiff$|\.tif$/i}readdir $target
+_dir;
my @video_files = grep{/^VID.+|\.3gp$|\.mp4$|\.avi$/i}readdir $target_
+dir;
[download]

Oh, I am a bit dubious about the "begins with VID" idea.