Patellofemoral joint (PFJ) issues affect one in four people, with 20% experiencing chronic knee pain despite treatment. Poor outcomes and pain after knee replacement surgery are often linked to patellar mal-tracking. Traditional imaging methods like CT and MRI face challenges, including cost and metal artefacts, and there's currently no ideal way to observe joint motion without issues such as soft tissue artefacts or radiation exposure. A new system to monitor joint motion could significantly improve understanding of PFJ dynamics, aiding in better patient care and outcomes. Combining 2D ultrasound with motion tracking for 3D reconstruction of the joint using semantic segmentation and position registration can be a solution. However, the need for expensive external infrastructure to estimate the trajectories of the scanner remains the main limitation to implementing 3D bone reconstruction from handheld ultrasound scanning clinically. We proposed the Visual-Inertial Odometry (VIO) and the deep learning-based inertial-only odometry methods as alternatives to motion capture for tracking a handheld ultrasound scanner. The 3D reconstruction generated by these methods has demonstrated potential for assessing the PFJ and for further measurements from free-hand ultrasound scans. The results show that the VIO method performs as well as the motion capture method, with average reconstruction errors of 1.25 mm and 1.21 mm, respectively. The VIO method is the first infrastructure-free method for 3D reconstruction of bone from wireless handheld ultrasound scanning with an accuracy comparable to methods that require external infrastructure.