Pluripotent stem cells, which include embryonic stem cells (ES cells) and induced pluripotent stem cells (iPS cells), have the ability to differentiate to tissues of all three germ layers: ectoderm, mesoderm, and endoderm. Many human pluripotent stem cell differentiation protocols begin with the formation of 3-dimensional aggregates of cells called embryoid bodies (EBs). Conventional EB formation methods involve scraping adherent ES cell and iPS cell cultures to release large clumps of cells, and placing the resulting aggregates in non-adherent suspension culture. Using these methods, the embryoid bodies formed are heterogeneous in size and shape, leading to inefficient and uncontrolled differentiation.