Mastering motor skills requires performing the task unconsciously with great speed and accuracy. This is acquired slowly through practice over time. Nonetheless, in domains such as surgery, the training of these skills in the field introduces safety, ethical and economic issues. In this context, immersive VR technologies offer the possibility to recreate real-world situations and allow the trainees to improve their skills in a safe and controlled environment. However, the design of such systems raises new research questions, such as how to represent the user in the virtual environment, and whether this representation can influence motor skills automaticity.In this work, we focus on how the user's hand representation can impact the training of tool-based motor skills in immersive VR. To investigate this question, we have created a VR simulator for training a tool-based pick and place task, and conducted a user study to evaluate how the user's hand visualization can influence participants' learning performance after a two-week training period. For that purpose, two groups of participants were trained in the VR simulator under one of the two experimental conditions: the presence and the absence of their virtual hands' representation, while a control group received no training. The results of the study show that training on the VR simulator improves the participants' motor task performance when compared with the control group. On the other hand, no difference was observed between the two training groups. This suggests that the user's hand visualization does not always impact tool-based motor tasks training in immersive VR simulators. Indeed, for short-term motor training there was no difference in performance between having a partial embodiment of the user's hands and only the tools representation.