Carbon nanotubes (CNTs) show superior mechanical and physical properties and seem to be promising ideal reinforcing material for polymer matrix composites of high strength and low density. In most of the experimental results till date, however, only modest or negligible improvements in stiffness and strength have been observed. The reason for less than expected improvements has been blamed on weak interfacial bonding of CNTs to the matrix, waviness in CNTs, and agglomeration of CNTs in resin at higher particle volume fractions. In this chapter, the effect of interfacial bonding, waviness, and agglomerations on the nanocomposite stiffness, Poisson’s ratio and strength are considered via numerical simulations. The proposed methodology combines the Mori-Tanaka effective field method, micromechanics, classical laminate theory (CLT) 262and multiscale progressive failure analysis (MS-PFA) to predict the desired material properties of nanocomposites without the need for time consuming and expensive testing. The results demonstrate the robustness of the methodology with the comparison against test data from literature without relying on extensive finite element modeling of CNTs within polymer matrix material.