We describe a strategy for regionalizing subnational administrative units in conjunction with harmonizing changes in unit boundaries over time that can be applied to provide small-area geographic identifiers for census microdata. The availability of small-area identifiers blends the flexibility of individual microdata with the spatial specificity of aggregate data. Regionalizing microdata by administrative units poses a number of challenges, such as the need to aggregate individual scale data in a way that ensures confidentiality and issues arising from changing spatial boundaries over time. We describe a regionalization and harmonization strategy that creates units that satisfy spatial and other constraints while maximizing the number of units in a way that supports policy and research use. We describe this regionalization strategy for three test cases of Malawi, Brazil, and the United States. We test different algorithms and develop a semi-automated strategy for regionalization that meets data restrictions, computation, and data demands from end users.