Dynamic stencil lithography uses a moving shadow-mask to draw patterns by having directionally evaporated material deposited through the stencil apertures onto the substrate. Sub-micrometre, two-dimensional patterning is demonstrated at full 100 mm wafer scale, with two examples emphasizing this technique's unique features. Structures having a width-modulated height below a certain aperture size are fabricated by moving the stencil according to a two-dimensional trajectory. Variable-period gratings are obtained by translating a row of apertures at different orientations with respect to the row's axis. Despite the long deposition sequences one could envision for a stencil in dynamic mode, the apertures' active life-time in the sub-micrometre domain remains limited by the material's accretion on the membrane, resulting in the eventual clogging of the openings. A novel solution to this problem containing a micro-heater embedded in the membrane is described and its effectiveness in preventing material from clogging the apertures is demonstrated.