Gaps in composite structures are a risky factor in aeronautical assemblies. For mechanically joined composite components, the geometrical conformance of the part can be problematic due to undesired or unknown re-distribution of loads within a composite component, with these unknowns being potentially destructive. To prevent unnecessary preloading of a metallic structure, and the possibility of cracking and delamination in a composite structure, it is important to measure all gaps and then shim any gaps greater than 127 microns. A strategy to overcome the high relative tolerances for assemblies lies in the automated manufacturing of shims for the gaps previously predicted through the evaluation of their volumes via a simulation tool. This paper deals with the development of a special end-effector prototype to enable the shimming of gaps in composites structures using a pre-processed geometry. The aim of this end-effector is to provide movement to a temperature controlled hot-end in order to generate a solid shim of ABS on the target composite surface. This process is defined according to the trajectories and velocities marked by the 3D printing process using standard G-code. The geometry and material volume to be printed are indicated by the simulated gap volume which is based on previous metrological measurements. The final objective will be to attach this end-effector to an anthropomorphic robot to enable autonomous manufacturing. This work is part of the EU FP7 funded LOCOMACHS project, under grant agreement n°314003.