So maybe something along these lines

use CGI 4.20;
use File::Copy qw/ copy /;

for my $key ( $cgi->all_parameters ){
    for my $fh( $cgi->upload( $key ) ){
        if(!$fh && $cgi->cgi_error ){
            print "<p> $fh got problem", $cgi->cgi_error, "\n";
            next;
        } else {
            binmode $fh;
            my $destFilename = "$destination/".WashFilename( "$fh" );
            
            copy( $fh, $destFilename )
                or die "Copy to ( $destFilename ) failed: (( $! ))(( $
+^E ))";
        }
    }
}
...
sub WashFilename {
    use File::Basename;
    my $basename = basename( shift );
    # untainted , only use a-z A-Z 0-9 and dot
    $basename = join '', $basename =~ m/([.a-zA-Z0-9])/g;
    # basename is now, hopefully, file.ext
    ## so to ensure uniqueness, we adulterate it :)
    my $id = $$.'-'.time;
    my( $file, $ext ) = split /\./, $basename, 2 ;
    return join '.', grep defined, $file, $id, $ext;
} ## end sub WashFilename
[download]

Works like a charm! Thanks :)

@filenames = param('files[]');

for ($filecount = 0; $filecount < @filenames; $filecount++)
{
    $upload_filehandle = upload('files[]');
    open ( UPLOADFILE, ">$upload_dir/$filenames[$filecount]" ) or die 
+"$!";
    binmode UPLOADFILE;
    while ( <$upload_filehandle> )
    {
        print UPLOADFILE;
    }
    close UPLOADFILE;       
}
[download]

see Re^2: How to save multiple uploaded files on the server?