In general,

One can take transverse section at inguinal region covering a nipple (Ref.- Exp. Pathology 55 : 2003).

However, if animals are treated/exposed with Dermal route, obviously, one need to consider treated area i.e. back. one can define the area on a sketch and follow it though your controls and treated consistently. 

optionally, one can take longitudinal plane i.e. along with hairs directions to study effects on hair roots etc....

(additional suggestion- place the skin piece flat on index card-hairs up and then immerse in fixative jar)

Best luck

Dr. Yogesh