This study demonstrates precise profile control of 3D lateral junction traps in silicon by exploiting a 2D mask layout and isotropic etching. The traps penetrate through silicon partitions and laterally link microfluidic channels. Since the trap constrictions cannot be registered directly by planar lithography, they are not trivial to define but critical for capturing cells in suspension. A special mask layout introduced here when combined with isotropic etching can form elliptic and circular constrictions. The mask layout offers three design parameters: two geometric angles and a separation distance between them. The design parameters have been systematically varied and a set of corresponding trap structures have been fabricated. Mapping of the constriction profiles to design parameters indicates that the constriction shape is mainly determined by the two design angles whereas the constriction size is controlled by the separation distance and total isotropic etching. It is shown that a circular constriction can be fabricated by setting the two angles such that their harmonic mean yields a critical value of about 45°. The constriction size may vary from several micrometers to tenths of micrometers depending on the separation distance and isotropically etched amount.