Upper limb amputation is often followed by a sensation that the affected limb is still present. This phantom limb representation is also reflected in the body image of the patient and can be associated with painful and non-painful sensations. Commonly, phantom limb appearance and pain is assessed with questionnaires, interviews and analogue drawings onto a 2D human outline. However, for patients it is hard to express the characteristics and sensations of the phantom limb and for clinicians it is challenging to compare and track patient testimonials. Our aim was to develop and evaluate a digital program to visualize phantom limb appearance and position, as well as pain and cramp hot spots of the phantom limb, on a 3D human model that represents the body image of the patient. Usability results show that a variety of upper limb impairments and pain areas can be adequately represented using this software. A 3D avatar is modeled after the patient’s body image and not only the appearance of the phantom limb itself can be depicted, but also its somatic abnormalities, such as telescoping. In addition, every dimension of the 3D model can be quantified, to not only provide a visual and qualitative analysis, but also quantifiable results for longitudinal analyses and comparison of different groups. Pain intensity and cramps can be drawn directly onto the rotatable 3D model to accurately reflect the patient’s perception. The 3D body image perception visualization tool CALA offers a novel and innovative computer-assisted method for the realistic representation of body, phantom limb and pain perception.