Thin and ultra-thin films of nickel phthalocyanine have been deposited in ultra-high vacuum on highly oriented pyrolitic graphite. The growth mode and the interaction with the substrate have been studied in situ by X-ray photoelectron spectroscopy, scanning tunneling microscopy and atomic force microscopy, and ex situ by means of tapping-mode atomic force microscopy. We present photoelectron spectroscopy measurements at various film thicknesses which show no detectable interaction of the adsorbed organic layers with the substrate, but, varying the deposited film thickness by in-situ annealing the substrate, we show desorption effects semiquantitatively described. The XPS spectrum of the C 1s multiplet structure of NiPC obtained using a monochromatized source is also presented. The scanning probe images presented address morphological issues like the growth mode at initial stages of deposition and at higher coverages. Moreover, upon annealing of the PC films, we show high-resolution measurements consistent with the low-size stable α crystalline phase of phthalocyanine molecules. The potential of tapping-mode atomic force microscopy in imaging soft adlayers deposited over soft substrates is addressed throughout the paper.