Controlled synthesis and integration of carbon nanotubes (CNTs) remain important areas of study to develop practical carbon-based nanodevices. A method of controlling the number of CNTs synthesized depending on the size of the catalyst was characterized using nanostencil lithography, and the critical dimension for the nanoaperture produced on a stencil mask used for growing individual CNTs was studied. The stencil mask was fabricated as a nanoaperture array down to 40 nm in diameter on a low-stress silicon nitride membrane. An iron catalyst used to synthesize CNTs was deposited through submicron patterns in the stencil mask onto a silicon substrate, and the profile of the patterned iron catalyst was analyzed using atomic force microscopy. The feasibility toward a scalable, number-, and location-controlled synthesis of CNTs was experimentally demonstrated based on the diameter and geometry of the apertures in the stencil mask.