I agree with Deb. I have worked with a large dermatology group (20+ providers) for years. These docs usually did a biopsy and then had the patient return when necessary. There were times when the assessment stated wart, scar or skintag but path came back as actinic keratosis or cancer.

So to answer the question at hand:
"My question is as a coder placing a cpt do we choose from the opinion of the MD at the time of the excision or do we wait for the pathology with definitive tissue diagnosis of the lesion? Sometimes this can be different when the physician only states lesion or mass and the pathology of the lesion defines pre cancerous cells or a definite cancer."

Everything I have ever read on the subject has stated that proper coding is to wait for pathology.