James T. Kirk completes a quarterly physical
Dr. Julian Bashir performs a physical on a replicant of Miles O'Brien
A physical was a full examination that assessed an individual's general health and wellbeing.
Physicals may be ordered at the discretion of the chief medical officer whenever necessary, including of the captain. Aside from ordered physicals starships also have regular physicals to monitor the regular health of the crew. In the 23rd century these physicals were done quarterly, but by the 24th century they were only performed annually. (TOS: "The Corbomite Maneuver"; TNG: "Allegiance")
According to Starfleet protocols, physicals are mandatory following away missions that last more than two weeks. (VOY: "Memorial")
Doctor Leonard McCoy conducted a quarterly physical on Captain James T. Kirk in 2266, just prior to the USS Enterprise's encounter with the Fesarius. (TOS: "The Corbomite Maneuver")
In 2267, McCoy had Nurse Chapel conduct a complete physical on Ensign Chekov. (TOS: "The Deadly Years")
During the 23rd century, doctors on Federation starships had the duty of performing quarterly physicals on each member of the crew. (TAS: "Yesteryear")
A perfect replica of Captain Jean-Luc Picard came in a month early for his physical in 2366. (TNG: "Allegiance")
Doctor Julian Bashir gave Miles O'Brien an extremely thorough physical when O'Brien was suspected of being a replicant. (DS9: "Whispers")
In 2371, The Doctor discovered that Ensign Samantha Wildman was pregnant during her annual physical, but she asked him to keep it from Captain Kathryn Janeway, as Wildman wanted to inform the captain personally. (VOY: "Elogium", "Fury")
In 2373, Bashir conducted a complete physical of Benjamin Sisko under orders of Admiral Charles Whatley. (DS9: "Rapture")
In 2375, The Doctor added deep-body scanning with his holographic imager as part of annual physicals on-board USS Voyager, allowing him to create images of his patients down to the subatomic level. Captain Kathryn Janeway, however, did not report for her physical, "as usual," forcing him to track her down in her ready room to administer her physical, with a request to drop by Sickbay at her earliest convenience to undergo the deep-body scan. (VOY: "Latent Image")