The operation was called Project Forsaken and the arrests were made from Tuesday through Thursday of last week, said Lt. Neil Haws, the director of the Region II Narcotics Task Force.
The majority of suspects were arrested at homes without incident, Haws said. Other arrests were made during traffic stops.
Local law enforcement spent about two weeks preparing to know when and where the suspects were going to be during the operation, Haws said.
Of the 41 people who were arrested, 11 people were taken into custody for selling methamphetamine and other drugs and 12 people were arrested for having outstanding warrants, the San Juan County Sheriff's Office announced Saturday evening.
"These were career criminals," Haws said. "There is the potential they could see several years in prison."
During the arrests, police seized a significant amount of illegal weapons, Haws said.
The San Juan County Sheriff's Special Enforcement Team, U.S Marshals and United State Department of Homeland Security agents assisted the local narcotics task force, which is comprised of sheriff's office and Farmington and Bloomfield police personnel, in making the arrests, Haws said.
"The operation was extremely successful," Haws said. "The federal partnership gives local law enforcement an additional tool in ridding our community of career criminal and repeat offenders."
On Tuesday of last week, Homeland Security agents arrested Wesley Eaton, 37, and Aaron Eaton, 31, at Wesley's home at 609 Pima Ave. in Farmington.
The brothers have long criminal histories that include burglaries, narcotics trafficking, battery and DWIs.
The federal agents seized 11 grams of methamphetamine, marijuana, prescription medicines, $4,000 in cash and illegal firearms from the home, Haws said.
On Wednesday, Homeland Security and local law enforcement agents arrested Bill Milligan, 26, during a traffic stop in San Juan County. Milligan was arrested for having a half-pound of marijuana and an illegal gun
Milligan has numerous felony arrests in San Juan County dating back more than 10 years for forgery, selling marijuana and identity theft.
Milligan and the Eatons may face federal charges, which would likely come with a longer prison sentence if convicted, Haws said.