The objective of the proposed research is to analyze the performance of designing a molecular computer. The performances are analyzed starting from molecular diodes to transistors, integrated chip, and very large scale circuit design with different organic materials. It overviews the properties like material compatibility, chemical registrant, dimension, temperature variation, specific heat, hybridization property, moulding shrinkage and tunneling effect etc. affect the performance in compare to our silicon level design. Further it enhance to DNA level design and analyze the advantages, disadvantages of various techniques of designing an optimum and powerful molecular computer with high speed and accuracy. Another objective of this research work to go for a total bench mark analysis to silicon based computer, organic molecule based computer and biological based DNA Computer with a paradigm approach to performance factors. It reflects a standard formula to go for a speed, accuracy and memory of processor taking into different performance factors.