You say it is out of level by 3mm is this from front to back or from side to side. This is a 40g breeder (36" x 18") correct?
Well either way it is fine 3mm is less then 1/8 of an inch. An 1/8 over 18" is no big deal, you need to do nothing with it. Heck your tank trim could be off that much, have you checked with a level?