Increase in applications of micro devices in MEMS and NEMS, demands efficient cooling systems. Due to miniaturization, the conventional cooling systems fail to satisfy the required cooling performance. Therefore design and analyses of optimized cooling system for different micro devices are required for its better performance. The present work investigates the conjugate heat transfer analysis in selected configurations of microchannels (rectangular, circular and trapezoidal with two configurations) with water as coolant. Three dimensional numerical simulations were performed using commercially available package ANSYS FLUENT 18.1. This work proposes a way to analyse the conjugate heat transfer properties in different microchannels cross sections. The steady state three-dimensional numerical simulations were carried out for single phase forced convection laminar flow. The present analyses focus on comparative study of heat transfer characteristics in different shape of the channels. The dimensions of microchannels were chosen by considering hydraulic diameter as constant in different geometrical shapes. The inlet velocities were varied as 1m/s, 1.5m/s, 2m/s, 2.25m/s, 2.5m/s and parameters such as Nusselt number, pressure drop and outlet temperature at constant heat input were determined and compared. It is revealed that geometrical shapes of microchannels have significant effects in the heat transfer characteristics.