This work presents a microwell prototyping technique for generating multicellular cancer aggregates in suspension culture for epithelial- mesenchymal-transition (EMT) drug screening. Microwell and aggregate size and geometry were examined in PMMA, PDMS, polystyrene materials materials. Retrieved aggregates were further studied in terms of cell dispersion through drug screening, to identify the effective drug dosage for the inhibition of EMT. Two distinct cell phenotypic behaviors were discovered from Low-attachment-dish- and microwell-generated aggregates under different conditions. Future studies of the two types of aggregates may contribute to the understanding of cancer metastasis.