Algorithmic efficiency and golf are not good friends. 33 chars, assuming you only want two prime factors:
  
sub factor {
  $n=$p=pop;1while$n%--$p;$n/$p,$p;
}

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Update: Thanks to CheeseLord for pointing out that the trailing semicolon on this golf is entirely unnecessary, without merit, sans raison d'etre, serving absolutely no purpose, whatsoever, amen. 
   MeowChow                                   
               s aamecha.s a..a\u$&owag.print

In reply to (MeowChow) Re: RSA Factoring challenge by MeowChow
in thread RSA Factoring challenge by one4k4

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