A baryon sweep in progress
A baryon sweep was a procedure used to eliminate baryon particles from a starship. The baryons accumulated as a natural side-effect of warp travel and generally needed to be removed every five years to keep harmful radiation from building up.
The sweep could be accomplished at specialized space stations such as the Remmler Array. The sweep was green in color and resembled a force field, capable of passing through solid matter. The strength of the sweep could be adjusted and made more effective for a ship which had made heavy use of its warp drive. The sweep was deadly to organic matter, and all lifeforms aboard a ship were evacuated to a safe location before the sweep was initiated. Additionally, the sweep could be damaging to certain areas such as the bridge and computer core, so field diverters could be installed in order to deflect the sweep and protect the sensitive equipment. Once the diverters were installed and the crew evacuated, an auto shutdown sequence was initiated, the ship powered down, and the sweep began. The sweep took a few hours to complete and was generally conducted from stern to bow.
The USS Enterprise-D docked at the Remmler Array for its first (and ultimately, only) sweep in 2369. It needed a stronger than usual sweep because it had spent more time at warp in five years than most ships did in ten. (TNG: "Starship Mine")
During his time at Starfleet Academy, Harry Kim would order baryon sweeps of his dorm room. In 2376, he told Lyndsay Ballard, his then-neighbor, that it was a consequence of "living across the hall from a slob". (VOY: "Ashes to Ashes")
Ensign Brad Boimler assisted with a baryon sweep of the USS Cerritos's warp nacelles in 2380. (LD: "Temporal Edict")
After the USS Cuyahoga returned to Federation Headquarters in 3189, Fleet Admiral Charles Vance ordered his chief of security Lieutenant Audrey Willa to commence a baryon sweep after the crew had cleared the ship. (DIS: "Scavengers")
Baryons include protons and neutrons, heavy subatomic particles that are a part of most normal matter. As practically all visible matter in the universe contains these then, a process which eliminates baryons wouldn't leave much of the Enterprise behind. We can assume that the baryon sweep removes dangerous concentrations of the particles or a certain variety created by the subspace field of the warp drive, rather than all of them found on the ship.