Cosmic-ray (CR) particles propagating in the Galaxy interact in the interstellar medium with gas, losing energy and producing secondary particles via inelastic losses and fragmentation. Obser- vations of the secondaries can be used to constrain the origin and propagation of the CRs, and may also provide signatures of new physics. To date CR propagation models have used the 2D Galactocentric cylindrical symmetry approximation for the spatial distribution of the interstellar gas. This is partly due to difficulties in uniquely determining its true 3D structure. In this contri- bution a method for determining the 3D spatial distribution of interstellar gas is described and first results using it to develop models that can be used in CR propagation codes like GALPROP are given. Implications for analysis of CR and γ-ray data using 3D spatial models for the interstellar gas are also discussed.