The paper gives a comprehensive study of inertial manifolds for semilinear parabolic equations and their smoothness using the spatial averaging method suggested by G. Sell and J. Mallet-Paret. We present a universal approach which covers the most part of known results obtained via this method as well as gives a number of new ones. Among our applications are reaction-diffusion equations, various types of generalized Cahn-Hilliard equations, including fractional and 6th order Cahn-Hilliard equations and several classes of modified Navier-Stokes equations including the Leray-$alpha$ regularization, hyperviscous regularization and their combinations. All of the results are obtained in 3D case with periodic boundary conditions.