Factor analysis is a powerful tool used for the analysis of dynamic studies. One of the major drawbacks of factor analysis of dynamic structures (FADS) is that the solution is not mathematically unique when only nonnegativity constraints are used to determine factors and factor coefficients. In this paper, a method to correct for ambiguous FADS solutions has been developed. A nonambiguous solution (to within certain scaling factors) is obtained by constructing and minimizing a new objective function. The most common objective function consists of a least squares term that when minimized with nonnegativity constraints, forces agreement between the applied factor model and the measured data. In our method, this objective function is modified by adding a term that penalizes multiple components in the images of the factor coefficients. Due to nonuniqueness effects, these factor coefficients consist of more than one physiological component. The technique was tested on computer simulations, an experimental canine cardiac study using 99mTc-teboroxime, and a patient planar 99mTc-MAG3 renal study. The results show that the technique works well in comparison to the truth in computer simulations and to region of interest (ROI) measurements in the experimental studies.