Nine members of the drug gang, all demobilized members of paramilitary organization AUC, were arrested in the raid.
According to a report by Bogota radio station Santa Fe, the "mother camp" was found in the Norte de Santander department in the north of the country.
A local police commander told the radio station that the authorities had been preparing the raid for three months and had used a spy plane to monitor the area.
Los Rastrojos is one of Colombia's leading drug gangs and an off-spring of the infamous Norte del Valle Cartel. The organization is primarily active in the south-west of Colombia.