Advances in nanotechnology enable scientists for the first time to study biological processes on a nanoscale molecule-by-molecule basis. They also raise challenges and opportunities for statisticians and applied probabilists. To exemplify the stochastic inference and modeling problems in the field, this paper discusses a few selected cases, ranging from likelihood inference, Bayesian data augmentation, and semi-and non-parametric inference of nanometric biochemical systems to the utilization of stochastic integro-differential equations and stochastic networks to model single-molecule biophysical processes. We discuss the statistical and probabilistic issues as well as the biophysical motivation and physical meaning behind the problems, emphasizing the analysis and modeling of real experimental data. Keywords: likelihood analysis, Bayesian data augmentation, semi-and non-parametric inference, single-molecule experiment, subdiffusion, generalized Langevin equation, fractional Brownian motion, stochastic network, enzymatic reaction MSC(2000): 60G35, 62F15, 62G05, 62P10, 92C05, 92C45