Fused deposition modeling 3D printing (3DP) has a potential to change how we envision manufacturing in the pharmaceutical industry. A more common utilization for FDM is to build upon existing hot melt extrusion technology where the drug is dispersed in the polymer matrix. However, reliable manufacturing of drug-containing FDM filaments remains a challenge along with the limitation of active ingredients which can sustain the processing risks involved in the HME process. To circumvent this obstacle, a single step FDM process was developed to manufacture thin-walled drug-free capsules which can be filled with dry or liquid drug product formulations. Drug release from these systems is governed by the combined dissolution of the FDM capsule ‘shell’ and the dosage form encapsulated in these shells. To prepare the shells, the 3D printer files (extension ‘.gcode’) were modified by creating discrete zones, so-called ‘zoning process’, with individual print parameters. Capsules printed without the zoning process resulted in macroscopic print defects and holes. X-ray computed tomography, finite element analysis and mechanical testing were used to guide the zoning process and printing parameters in order to manufacture consistent and robust capsule shell geometries. Additionally, dose consistencies of drug containing liquid formulations were investigated in this work.