Flax seed(Linseed, Linum usitatissimum L.) and its oil, a richest source of alpha-linolenic acid(ALA)(${omega}-3$), contain saturated fatty acids, neurotoxic cyanogen glycosides and immuno-suppressive cyclic-nonapeptides. Present paper describes the development of two chemical processes, Process-A and -B, to remove saturated fatty acids and to destroy cyclic nonapeptides and cyanogen glycosides from flax seed oil. Process-A consists of three major steps, i.e., extraction of fatty acid mixture by alkaline saponification, removal of saturated fatty acid by urea-complexation, and triglyceride reconstruction of unsaturated fatty acid via fatty acyl-chloride activation using oxalyl chloride. Process-B consists of preparation of fatty acid ethyl ester by transesterification, elimination of saturated fatty acid ester by urea-complexation, and reconstruction of triglyceride by interesterification with glycerol-triacetate (triacetin). The destruction of lipophilic cyclic nonapeptide during saponification or transesterification processes could be demonstrated indirectly by the disappearance of antibacterial activity of bacitracin, an analogous cyclic-decapeptide. The cyanogen glycosides were found only in the dregs after hexane extraction, but not in the flax seed oil. The reconstructed triglyceride of flax seed oil, obtained by these two different pathways after elimination of saturated fatty acid and toxic components, showed agreeable properties as edible oil in terms of taste, acid value, iodine and peroxide value, glycerine content, and antioxidant activity.