Abstract-Assessment of upper extremity motor skills often involves object manipulation, drawing or writing using a pencil, or performing specific gestures. Traditional assessment of such skills usually requires a trained person to record the time and accuracy resulting in a process that can be labor intensive and costly. Automating the entire assessment process will potentially lower the cost, produce electronically recorded data, broaden the implementations, and provide additional assessment information. This paper presents a low-cost, versatile, and easy-to-use algorithm to automatically detect and track single or multiple well-defined geometric shapes or markers. It therefore can be applied to a wide range of assessment protocols that involve object manipulation or hand and arm gestures. The algorithm localizes the objects using color thresholding and morphological operations and then estimates their 3-dimensional pose. The utility of the algorithm is demonstrated by implementing it for automating the following five protocols: the sport of Cup Stacking, the Soda Pop Coordination test, the Wechsler Block Design test, the visualmotor integration test, and gesture recognition.