Novel magnetic materials in the family of B20 crystal structures exhibiting skyrmions have been shown to have great potential for use in magnetic storage and logic due to their ultra-high storage density and low critical current for switching compared to present technologies. Using aberration corrected in situ Lorentz transmission electron microscopy (LTEM) and scanning transmission electron microscopy (STEM), we investigate the effects of microstructure on magnetic skyrmion structure in B20 FeGe thin films grown on Si(111) by molecular beam epitaxy. In the noncentrosymmetric B20 system, crystallographic chirality can lead to both right- and left-handed magnetic chirality in the skyrmions, which can be directly imaged and quantified using LTEM. The effects of grain boundaries and the substrate/film and film/vacuum interfaces are also explored through a combination of LTEM and atomic resolution STEM. Understanding the effects of crystallographic chirality on magnetic structure is a critical step towards device application for skyrmion materials.