A biomolecular scan was a medical scan.
In 2152, Doctor Phlox performed a full biomolecular scan on Ensign Travis Mayweather as his previous scans had shown no results. (ENT: "Singularity")
When Hoshi Sato went missing after a transporter accident, Doctor Phlox compared his two biomolecular scans of Sato which seemed to be perfectly normal. (ENT: "Vanishing Point")
In 2371, Chief Miles O'Brien ran a biomolecular scan security chief Odo asked for. He found living tissue on the bulkhead around the blast site of Garak's tailor shop. (DS9: "Improbable Cause")
The same year, The Doctor performed a biomolecular scan on Tom Paris to further investigate his amnesia. (VOY: "Cathexis")