With recent developments in micro and nano-technologies, mechanical components such as those used in medicine or electronics tend to be miniaturized, requiring a new set of testing techniques to study their reliability and performance. One of the new methods is micro-pillar compression testing, which allows the study of mechanical properties of confined volumes precisely shaped by focused ion beam (FIB) milling from sometimes complex microstructures. This technique has garnered a great deal of interest in recent years; on one hand because of its apparent simplicity, on the other hand because it revealed an unexpected size dependence in the flow stress of single crystals when the pillar diameter was reduced below a few tenths of a micrometre. The flow stress of FIB milled face centred cubic (fcc) micro-pillars appears to follow a power law as a function of their size. In contrast, non-FIB milled, body centred cubic (bcc) eutectic Molybdenum (Mo) alloy pillars prepared by directional growth exhibit, in their pristine state, whisker-like behaviour without a size effect. Furthermore, after FIB milling or moderate pre-deformation, the whisker character is lost and the typical scatter of the flow stress usually observed for FIB milled pillars is reproduced. After large pre-deformation the scatter vanishes and the pillars exhibit no size effect. These findings show that 1) the deterministic parameter in the size effect can be correlated with the initial microstructure of the pillar, and 2) FIB milling influences this microstructure. This study aims to link the deformation modes occurring in small-scale pillars with their initial microstructure by studying directionally solidified eutectic Mo-alloy pillars with a diameter of 1 micrometre. In-situ Laue diffraction experiments during the compression of such defect-free pillars show that with readily-available dislocation sources from a concave pillar top, the {112}[111] slip system with the highest Schmid factor is initially activated and not the allegedly assumed {110}[111] slip system that is typical for bcc metals. Post-mortem slip trace analysis and TEM observations confirm this finding. Moreover, 3D atom probe measurements and TEM images show that this behaviour can be linked to the presence of both alloying elements and fcc nano-precipitates found in the bcc Mo-alloy. Both can lead to a decrease of the critical temperature and the observation of an fcc-like deformation. Additionally, it is shown that both FIB milling and pre-deformation introduce defects in the initially dislocation-free pillars. In addition to this, pillars prepared under similar conditions yield quite different microstructures. The angle between the focused ion beam and the crystal orientation is found to play an important role in the creation of defects. It can also be shown that pillars with high initial dislocation density deform bulk-like and exhibit strain hardening, while pillars with low initial dislocation content demonstrate a large scatter in the flow and yield stress and exhibit large strain burst at later deformation stages. Furthermore several slip systems are activated before the flow stress is reached for pillars containing initially low dislocation content. Interestingly the first activated slip system can be linked to the initial streaking direction; slip is observed on the {112} plane that contains excess dislocations. For both the as-prepared pillars and the pillars with low initial dislocation content, the yield seems to be source limited, which is not the case for pillars with high initial dislocation content.