As technology scales, increasing interconnect costs make it necessary to consider alternate ways of building integrated circuits. One promising option along this direction is 3D architectures where a stack of multiple device layers, with direct vertical tunneling through them, are put together on the same chip. In this paper, we explore how processor cores and storage blocks can be placed in a 3D architecture to minimize data access costs under temperature constraints. This process is referred to as the topology exploration. Using integer linear programming, we compare the best 2D placement with the best 3D placement, and show through experiments with both single-core and multi-core systems that the 3D placement generates much better results (in terms of data access costs) under the same temperature bounds. We also discuss the tradeoffs between temperature constraint and data access costs.