The recent developments in devices that certify the quality of life increases the significance of microchannel heat transfer and fluid flow. The biomedical applications and micro-heat-exchangers are some of the examples where basics of the microchannel heat transfer and fuid flow are necessary for a suitable design of these devices. In first part of this study numerical simulation of heat transfer in smooth microchannels and have been investigated. In smooth microchannel, viscous dissipation and axial conduction heat transfer have been considered. The Navier-Stokes and energy equations are developed using perturbation expansion. The governing equations are solved with second-order velocity slip and temperature jump boundary conditions. In this method we developed pressure, temperature and velocity with using perturbation expansion and different orders of equations depending on the magnitude of Knudsen number are obtained. Equations are solved using finite volume method (FVM) and SIMPLE algorithm are used to solve governing equations.The flow is assumed to be steady, laminar and incompressible with constant properties in microchannel. Both constant heat flux and constant wall temperature boundary conditions are investigated. With constant wall temperature boundary conditions in fully developed region Nu number with viscous dissipation is larger than Nu number without viscous dissipation. In addition fully developed Nu number does not depend to Br Number when Br number is not equal to zero.With constant heat flux boundary conditions and in fully developed region, when Br number positive (heating condition), Nu number decreases with Br number, But when Br number is negative (cooling condition), Nu number increases with Br number. Results show that the effects of viscous dissipation in microchannels can not neglect. Present work confirms that the perturbation method is capable to predict viscous dissipation effects and the results are in good agreement with other works, when Kn number is less than 0.1. So for high Kn number we should use more term in perturbation expantions. In second part of this study, fluid flow and heat transfer has been simulated in a rough microchannel. We use rectangular element between tow parallel plates. In rough microchanel the boundary conditions considering constant wall temperature. For rough microchannel the Poiseuille number and Nu number for gas slip flow evaluated. In rough michannel the effects of viscous dissipation is neglected and consider axial conduction heat transfer. We also investigate effect of roughness on velocity profile. The effects of roughnes high, space between elements of roughnes, length of roughness elements, Re number and Kn number on slip behavior of gas flow in microchannels are investigated. The results compared with a smooth microchannel, the result show surface roughness elemets decreases boundary slip in wall of channels and cause average of Po number and Nu number increases and velocity profiles change. In rough microchannels and smooth microchannels Po number and Nu number both of them decreased as Kn number increases. In smooth microchannels if Re number increase the Po number and Nu number remains constand, but in rough microchannels increasing of Re number increases Po number and Nu number. In real simulation we should consider roughness surfaces and we can not neglect effects of roughness on fluid flow and heat transfer. Results show the perturbation method can predict effects of roughness on fluid flow and heat transfer and have good agreement with other works. Keywords: Heat transfer, slip-flow, micro-channel, roughness, viscous dissipation, perturbation expansion.