I believe that the primary speed problem is due to you opening and closing the output file in your cleaning loop. You should open the file before starting the loop, then write out all your data, and close at the end:

print "[-] Cleaning...\n";
open(OUTPUT,">>cleaned.txt") or die "Can't open cleaned.txt!";
foreach $data (@file1) {
    ($w1) = split(/:/,$data);
    print OUTPUT $w1."\n" unless ($data =~ /-/);
}
close(OUTPUT) or die "close error";
[download]

A couple of minor items:

• Always check your file operations (the or die "msg" bits above) to ensure that they were successful.
• If cleaned.txt is a "valuable" file, you should probably delete it only after successfully building your new one. You could, for example, build the file as cleaned.txt.tmp. Then, only after the final close is successful, you could rename cleaned.txt to cleaned.txt.bak and then rename cleaned.txt.tmp to cleaned.txt.

...roboticus

UPDATE: Fixed a bit of awkward grammar, added some formatting for readability.