The important applicational area of jute flax-based polymer composite being the automotive and wall panels. In comparison with the synthetic fibres used in the fabrication of composites, the jute flax fibres can be of great mechanical competent if treated properly with necessary chemicals modifications. In the application of automotive panels even though the jute flax based PMCs are manufactured to a near required shape, the secondary cutting process like drilling is essential for having a joint in an assembly. While performing the drilling process the composite undergo several types of damages including, delamination, cylindricity errors, fibre pull out, matrix cracking, surface roughness and also flank wear concerned with the tool etc. It is thus required to obtain the pure optimal set of parameters while performing drilling operation to control and reduce such damages to the composite as well as the tool. In this work an attempt is made to optimize the parameters involved in machining (drilling) of jute flax based composites in order to minimize the surface roughness and flank wear.