Biodiesel is an alternative fuel for diesel engines which is defined as a fuel comprised of mono alkyl ester of long chain fatty acids produced by chemically reacting a vegetable oil or animal fat with an alcohol such as methanol. Because of high cost of edible vegetable oils such as canola, soybean, and corn, it seems that commercialization of biodiesel production from edible oil is not economically favorable, while using waste oils as the feedstock, which is much less expensive than edible vegetable oil, can reduce the costs of biodiesel production. The homogeneous alkaline and acidic catalyst processes have complex and energy-consuming separation and purification steps. Supercritical methanol is a method of transesterification reaction without the presence of catalyst.in the process. The absence of catalyst in the process, leads to simpler separation and purification steps of biodiesel. The Response Surface Methodology was applied to analyze the effect of four independent variables (weigh ratio of methanol to oil, reaction temperature, pressure and flow rate) on the yield of the biodiesel production in supercritical methanol method. Hexane was used as a co-solvent, Waste fish oil was used as raw material and transesterification reaction was performed in a supercritical Continuous reactor. The optimal values of variables were determined by RSM to be 22.3:1 (methanol/oil weigh ratio) 270 o C, 112.7 bar and 2 ml.min - 1 flow rate for the maximum predicted yield of 94.6% (g/g). In the second part: the isolation of mono- unsaturated fatty acids, saturated and unsaturated fatty acids using urea complex in optimal conditions at 25°C and a weight ratio of urea to fatty acid was three to one. Palmitic acid purification to (78%) by combination of low temperature in the presence of solvents acetone and urea complexation was done.