The paper describes methods and fast computational algorithm for building effective Hamiltonians in molecular physics using perturbative approach. Various techniques of separation of fast and slow variables are considered in the general mathematical framework of contact transformations. The particular focus is on a systematic derivation of effective models for vibration-rotation spectroscopy from ab initio based potential energy surfaces with an exhaustive review of the previous studies in this field. We consider applications to various types of polyads coupled by Fermi, Coriolis, Darling-Dennison and other types of resonance interactions with the examples for asymmetric top, symmetric top and spherical top molecules. A flexible choce of the modelling operator accounts for strong coupling of various types of nuclear motion in molecules among closely lying levels including vibrational resonance schemes (2:1:2) , (2:1:2:1), (4:2:6:3), (3:2:1:2:1:1) etc that occur for C2v, C3v, and Td molecules and their isotopic species. The method is implemented in the MOL_CT program suite that offers a complementary tool to variational methods in terms of convergence and computational time. This permits an inclusion of a priori information to obtain physically meaningful values for the the resonance coupling terms in order to developing mixed "ab initio/effective" models with smaller number of adjustable parameters for analyses of molecular spectra.