Contrary to popular notion, pathologist does not only examine blood, urine & semen. They also do FNACS, biopsies & Bone marrow examination along with pre, intra & post-operative tissue examination. Based on the findings, the most probable diagnosis is made.
Sometimes further advanced investigation (IHC/molecular) or repeat investigation is advised. The microscope is the primary tool for a pathologist, along with so many other minor & major instruments.