In this paper we present an efficient algorithm to produce a provably dense sample of a smooth compact affine variety. The procedure is partly based on computing bottlenecks of the variety. Using geometric information such as the bottlenecks and the local reach we also provide bounds on the density of the sample needed in order to guarantee that the homology of the variety can be recovered from the sample. An implementation of the algorithm is provided together with numerical experiments and a computational comparison to the algorithm by Dufresne et al. [Sampling real algebraic varieties for topological data analysis, arXiv:1802.07716, 2018].