Determination of complex permittivity of bio-chemical fluid samples have been numerically investigated. The samples have been placed within a rectangular W-band waveguide enclosed in nanolitre volume microfluidic pipes. The effect on the S-parameters is observed by changing the shape, diameter, depth, and complex permittivity of the pipe inside the waveguide. Pipe depth and pipe diameter has a direct influence on the drop in transmission coefficient S21. The system shows the viability of measurements of liquid samples inside a waveguide at these frequencies. Extraction of the permittivity is not covered in this paper, however matching of experimental results to empirical dependences obtained by full wave electromagnetic solver is one method which can be used.