In this article, we address the nanofabrication process of self-organized, three-dimensional (3D) epitaxial oxide nanorods of perovskite La1-xSrxMnO3 and fluorite Gd2Zr2O7 using pulsed laser ablation. These nanorods are epitaxially gown on (001) LaAlO3 substrate and are well defined with a very narrow size distribution as studied by transmission electron microcopy. All of the nanorods are encapsulated by uniformly thick amorphous-like boundaries. The nanofabrication process leading to formation of 3D nanorods in these systems is discussed by considering the interplay of misfit strain energy and surface energy contributions. (c) 2005 Elsevier B.V. All rights reserved.