The manufacturing process of bone scaffold structures has an important influence on the final mechanical strength of the structure. When the structures are not produced properly, i.e. have imperfections such as missing parts or slightly displaced joints, they lose some of their mechanical properties. The aim of this study was to see how different types of damage affect the structures and also if their effects are equal when the structure is subjected to different load conditions. The change of the mechanical behavior was determined using the commercial finite element software MSC Marc Mentat. In turn, the damage was introduced by manipulating the structure’s files (ASCII data files) using the programming language Fortran. Apart from the numerical simulations, experimental testing was also performed to verify the numerical results. In the frame of this study, useful information for further research is provided.