In this work we present an efficient procedure to evaluate effective pair potentials, compatible with "experimental" structure factors, using a Monte Carlo simulation scheme. The procedure does not require the use of inverse Fourier transforms and is robust and rapidly convergent. As a test case the structure factor of liquid Selenium obtained from a Tight-Binding Molecular Dynamics simulation is inverted to obtain an effective pair potential and, as a by-product, the pair distribution function. The inversion procedure yields a pair structure in perfect agreement with the original molecular dynamics calculations and the analysis of the triplet structure and the dynamics also illustrates the limitations of the use of pair potentials in the description of liquids with strongly directional bonding, such as the covalent liquid Selenium.