Fe(x)Ge(1-x) superlattices with two types of nanostructures, i.e. nanodots and nanolayers, were successfully fabricated using low-temperature molecular beam epitaxy. Transmission electron microscopy (TEM) characterization clearly shows that both the Fe(x)Ge(1-x) nanodots and nanolayers exhibit a lattice-coherent structure with the surrounding Ge matrix without any metallic precipitations or secondary phases. The magnetic measurement reveals the nature of superparamagnetism in Fe(x)Ge(1-x) nanodots, while showing the absence of superparamagnetism in Fe(x)Ge(1-x) nanolayers. Magnetotransport measurements show distinct magnetoresistance (MR) behavior, i.e. a negative to positive MR transition in Fe(x)Ge(1-x) nanodots and only positive MR in nanolayers, which could be due to a competition between the orbital MR and spin-dependent scatterings. Our results open a new growth strategy for engineering Fe(x)Ge(1-x) nanostructures to facilitate the development of Ge-based spintronics and magnetoelectronics devices.