Observations show that MHD waves are one of the most important universal processes in the heliosphere. These waves are likely to play an important role in energy transfer in the heliosphere, and they can be used as a diagnostic tool of the properties of the local magneto-fluid environment. Recent observations by TRACE and Hinode satellites provide ample evidence of oscillations in coronal active region loops. The oscillations were interpreted as fast (kink), slow, and Alfvén modes, and the properties of the waves were used for coronal seismology. However, due to the complex interactions of the various modes in the inhomogeneous active region plasma, and due to nonlinearity, idealized linear theory is inadequate to properly describe the waves. To overcome this theoretical shortcoming we developed 3D MHD models of waves in active region loops. We investigated the effects of 3D active region magnetic and density structure on the oscillations and the wave dissipation, and we investigated the oscillation of individual loops. Some loops were constructed to contain several threads and twist. Here, we present the results of our models, and show how they can be used to understand better the properties of the waves, and of the active regions.