Generally for oil extraction, soxhlet extraction is used. Wherein, source material will be packed in the thimble and kept in Soxhlet unit. As you have small amount of sample, you can pack your sample (in powder form) in hand made filter paper pack and keep in Soxhlet unit. You have not mentioned the name of solvent. But I suggest you to use Hexane as a solvent for oil extraction. By this way you will not have any other material in oil sample. Then, you can go for direct transesterification as you have mentioned.    

 Dear Mrs M R Rathod,

Thank you for your answer. The problem with Soxhlet extraction is that I can't process samples simultaneously. I use methanol-HCl-chloroform mixture. And direct transesterification means that extraction and transesterification takes place at the same time, not one after the other.

It will be better if you extract the oil first as suggested and then transesterify with your method to esterify all the fatty acid present in your oil sample & you will get the better/ possibly true result.

Extraction of Lipids in Solution by the Method of Bligh & Dyer

(Bligh,E.G. and Dyer,W.J. 1959. A rapid method for total lipid extraction and purification.

Can.J.Biochem.Physiol. 37:911-917.)

Thx for the suggestions. In the meantime I have figured out that bead beating with methanol as solvent makes a perfect job for fungal cell disruption. I use a machine with 24 tube capacity.