Hi Sivtec,
What I would do is this - Insert a shim between the cutter and work and bring the axis into contact, the shim will be vertical when the height is correct, zero the Z Axis. Now with a cigarette paper on the work and cutter running approach the work (X or Y Axis - which ever you are using for depth of cut) until the paper is touched, zero this axis.
Cut the first tooth and inspect, if necessary increase the depth using the axis scale function ( scale 1.100 for example) and when it looks correct then cut the remainder.
I apologize if this is too basic.
Regards, Tweakie.