By analysing models of the young massive cluster R136 in 30 Doradus, set-up using the herewith introduced and publicly made available code McLuster, we investigate and compare different methods for detecting and quantifying mass segregation and substructure in non-seeing limited N-body data. For this purpose we generate star cluster models with different degrees of mass segregation and fractal substructure and analyse them. We quantify mass segregation by measuring, from the projected 2d model data, the mass function slope in radial annuli, by looking for colour gradients in radial colour profiles, by measuring Allisons Lambda parameter, and by determining the local stellar surface density around each star. We find that these methods for quantifying mass segregation often produce ambiguous results. Most reliable for detecting mass segregation is the mass function slope method, whereas the colour gradient method is the least practical in an R136-like configuration. The other two methods are more sensitive to low degrees of mass segregation but are computationally much more demanding. We also discuss the effect of binaries on these measures. Moreover, we quantify substructure by looking at the projected radial stellar density profile, by comparing projected azimuthal stellar density profiles, and by determining Cartwright & Whitworths Q parameter. We find that only high degrees of substructure affect the projected radial density profile, whereas the projected azimuthal density profile is very sensitive to substructure. The Q parameter is also sensitive to substructure but its absolute value shows a dependence on the radial density gradient of the cluster and is strongly influenced by binaries. (abridged)