We explore lithographic patterning and substrate orientation of single-crystal Ru substrates as the means to control shape, alignment, and magnetic anisotropy of epitaxial Co and Fe islands. The Co dots and stripes were grown at 350°C via molecular-beam epitaxy and characterized ex situ with atomic force microscopy, magnetic force microscopy, and the magneto-optic Kerr effect. For Co deposited onto a Ru͑0001͒ pre-etched with deep 6ϫ6 m squares, Co islands decorate the edges of the patterns and exhibit in-plane magnetic domains with easy axis along the edges. Shallow patterns, however, do not result in preferential positioning of the dots. When the etched shallow lines are along the close-packed ͓101 0͔ direction, the islands tend to elongate along the induced steps, which introduces a magnetic easy axis along the line direction. In contrast to the quasihexagonal dots of Co on Ru͑0001͒, Fe deposited on the twofold Ru(101 1) forms elongated islands of ϳ100 nm long and 20 nm wide.