Within the PANDA experiment, proton anti-proton collisions will be studied in order to gain knowledge about the strong interaction. One interesting aspect is the production and decay of charmed hadrons. The charm quark is three orders of magnitude heavier than the light up- and down-quarks which constitue the matter we consist of. The detection of charmed particles is a challenge since they are rare and often hidden in a large background. There will be three different targets used at the experiment; the cluster-jet, the untracked pellet and the tracked pellet. All three targets meet the experimental requirements of high luminosity. However they have different properties, concerning the effect on beam quality and the determination of the interaction point. In this thesis, simulations and reconstruction of the charmed D-mesons using the three different targets have been made. The data quality, such as momentum resolution and vertex resolution has been studied, as well as how the different targets effect the reconstruction efficiency of D-meson have been analysed. The results are consistent with the results from a similar study in 2006, but provide additional information since it takes the detector response into account. Furthermore, a new target distribution have been implemented in the software package. This is the first results obtained from a cylindrical target distribution. The results are very important for PANDA since they show the limitations of different target types regarding the possibilities to reduce background. Simulations with the new target distribution have been made for all three targets and the results are presented.