In this work, supercritical CO2 extraction for defatting of annatto seeds was studied; the objective was to obtain an extract rich in tocotrienols and the defatted rich-bixin seeds. The process conditions were selected from global yield isotherms assays performed at 313 and 333 K, and 20, 31, and 40 MPa; the ratio of solvent mass (S) to feed mass (F) was 35. For this S/F the highest extraction yield was 22 mg of extract/g dried seeds obtained at 333 K and 40 MPa. At these conditions a kinetic experiment was done to estimate the required parameters needed to estimate the cost of manufacturing (COM). COM was estimated using a commercial simulator; the model SFE plant had two extractor vessels in order to simulate continuous operation. A pilot plant size unit and two industrial size units were considered. The COM decreased from 124.58 to 109.27 US$/kg of extract as the extraction vessels capacities increased from 0.1 and 0.5 m3; for the pilot plant with 2 vessels of 0.005 m3 the COM was 300.00 US$/kg of extract.