In 3D freehand ultrasound imaging, operator dependent variations in applied forces and movements can lead to errors in the reconstructed images. In this paper, we introduce an automated 3D ultrasound system, which enables acquisitions with controlled movement trajectories by using motors, which electrically move the probe. Due to integrated encoders there is no need of position sensors. An included force control mechanism ensures a constant contact force to the skin. We conducted 8 trials with the automated 3D ultrasound system on 2 different phantoms with 3 force settings and 10 trials on a human tibialis anterior muscle with 2 force settings. For comparison, we also conducted 8 freehand 3D ultrasound scans from 2 operators (4 force settings) on one phantom and 10 with one operator on the tibialis anterior muscle. Both freehand and automated trials showed small errors in volume and length computations of the reconstructions, however the freehand trials showed larger standard deviations. We also computed the thickness of the phantom and the tibialis anterior muscle. We found significant differences in force settings for the operators and higher coefficients of variation for the freehand trials. Overall, the automated 3D ultrasound system shows a high accuracy in reconstruction. Due to the smaller coefficients of variation, the automated 3D ultrasound system enables more reproducible ultrasound examinations than the freehand scanning. Therefore, the automated 3D ultrasound system is a reliable tool for 3D investigations of skeletal muscle.