#!/usr/bin/perl -CS
use CGI;
use CGI::Carp qw(fatalsToBrowser);
my $cgi = new CGI;

my $filename = $cgi->param('file');
my $fh = $cgi->upload('file');
binmode $fh;

open(OUTPUT, ">/var/www/mypath/$filename") or die $!;
while(<$fh>) {
        print OUTPUT $_;
}

print $cgi->header();
print "$file has been successfully uploaded... thank you.\n";
[download]

• Don't use :utf8 on untrusted data. Use :encoding(UTF-8). For that matter, don't use :utf8.

• You decode bytes to chars, but you never encode the chars back to bytes when writing them. You'll get wide character warnings for non-ASCII chars, and you could get a mix of iso-latin-1 and UTF-8 characters in more complex programs.

• What awful inconsistency in your file handle names: $fh and OUTPUT? And using a global variable too?

Fixed:

...
my $fh_in = $cgi->upload('file');
binmode $fh_in, ':encoding(UTF-8)';

open(my $fh_out, '>:encoding(UTF-8)', "/var/www/mypath/$filename")
   or die $!;

while (<$fh_in>) {
   print $fh_out $_;
}
[download]

But there's absolutely no reason to convert to chars in the above code, so you'd be better off as

...
my $fh_in = $cgi->upload('file');
open(my $fh_out, '>', "/var/www/mypath/$filename")
   or die $!;

while (<$fh_in>) {
   print $fh_out $_;
}
[download]

You also mentioned binary uploads (like MP3s). For that, you'd use

...
my $fh_in = $cgi->upload('file');
open(my $fh_out, '>', "/var/www/mypath/$filename")
   or die $!;

binmode $fh_in;
binmode $fh_out;

local $/ = \4096;  # Don't wait to find "\n"
while (<$fh_in>) {
   print $fh_out $_;
}
[download]

The code for binary files also works with text files.