David Simon goes into detail about the basement in chapter 8. It is where the pathologists dissect the dead bodies. Simon says that for years, it was a disorganised chaotic place where the officers and the doctors, despite their differences, drank beer and smoked cigarettes. Sometimes they placed the bodies on the floor.
This changed when the basement was taken over by the medical examiner John Smialek. His more professional approach transformed it into what the detectives now refer to it as the Office of the Chief Medical Examiner.
If it all goes well, the corpses arrive in the basement in the same condition the detectives found them in at the crime scene. The pathologists weigh them before putting them onto a metal gurney and rolling them under an overhead camera. They then take photographs of the body before taking it into the autopsy area. They examine the clothes, removing them slowly whilst picking off any traces of evidence. Once the body is naked, the pathologist starts to look for anything on the body that looks out of place or is missing.
Once they finish the external examination, the pathologists start the autopsy. They have equipment such as saws and knives to open up the body. Simon says that, unlike most places, they don't have any recording equipment, so they have clipboards and paper to take their notes.