what primarily makes it difficult to observe the process of star formation
The structure of the molecular cloud and the effects of the protostar can be observed in near-IR extinction maps (where the number of stars are counted per unit area and compared to a nearby zero extinction area of sky), continuum dust emission and rotational transitions of CO and other molecules; these last two are observed in the millimeter and submillimeter range. The radiation from the protostar and early star has to be observed in infrared astronomy wavelengths, as the extinction caused by the rest of the cloud in which the star is forming is usually too big to allow us to observe it in the visual part of the spectrum. This presents considerable difficulties as the Earth's atmosphere is almost entirely opaque from 20μm to 850μm, with narrow windows at 200μm and 450μm. Even outside this range, atmospheric subtraction techniques must be used.