My rewrite is pretty similar to DBX's.

The main points:

• always, ALWAYS, use strict and -w,
• you use arrays in a lot of places where you really should be using scalars,
• you don't need a hash (%where if you are only going to ever use it's keys, you can use an array instead,
• you had 2 nested loops, where the second one (the foreach should really be outside. Actually you don't even need that extra loop, you can just do the find if the uid is a user uid,

#!/usr/bin/perl -w
use strict;

# better to have it as a clearly defined parameter
# mine is 500 for example
my  $MIN_USER_UID = 1000;

$|++;

open PASSWD, '/etc/passwd';
my @user;
while (<PASSWD>){
  my @field = split /:/;
  system ("find '/home/u1'  -user $field[0] -print >$field[0]") if($fi
+eld[2] > $MIN_USER_UID);
  }
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