The three-dimensional (3D) clustering of Janus cylinders is controlled by simply tuning the cylinder geometry and hydrophobic interactions. Janus cylinders were prepared by combining two approaches: micromolding and initiated chemical vapor deposition (iCVD). Hydrophilic cylinders with a flat- or convex-top curvature were prepared by micromolding based on surface tension-induced flow. The iCVD process then provides a hydrophobic domain through the simple and precise deposition of a polymer film on the top surface, forming monodisperse Janus microcylinders. We use these Janus cylinders as building blocks to form 2D or 3D clusters via hydrophobic interactions in methanol. We investigate how cylinder geometry or degree of hydrophobic interaction affects the resulting cluster geometries. The convex-top Janus cylinders lead to 3D clustering through tip-to-tip interactions, and the flat-top Janus cylinders lead to 2D clustering through face-to-face attraction. The number of Janus cylinders in 3D clusters is tuned by controlling the degree of hydrophobic (or hydrophilic) interaction.