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Micro-computed tomography (MCT) provides a tool for creating three-dimensional images of a sample by combining a series of two-dimensional "slices" of the object. This capability has led to an increasing number of applications of MCT data in research, including non-destructive evaluation and three-dimensional reconstructions of objects. However, a lack of standardization in the imaging process may lead to inconsistent results if the researcher is not aware of the factors which impact the resolution, detail, and density accuracy of the scan. This work addresses the variability present in the Xradia MCT-400 data and suggests techniques for controlling that variability. Sample preparation, including size, placement, and composition, imaging parameters such as threshold values, x-ray sample counts, scan resolution, and conversion of the output format for subsequent use of the data are discussed in the context of non-destructive evaluation of weld quality for friction stir welding of aluminum, but are universal for all applications. This work was performed in part during the Research Experience for Undergraduates (REU) hosted at SDSM&T in the summer of 2013. [ABSTRACT FROM AUTHOR]