We have measured the interaction between $^4$He gas at 4.2$~$K and a high-quality nano-electro-mechanical string device for its first 3 symmetric modes (resonating at 2.2$~$MHz, 6.7$~$MHz and 11$~$MHz with quality factor $Q > 0.1$ million) over almost 6 orders of magnitude in pressure. This fluid can be viewed as the best experimental implementation of an almost-ideal monoatomic and inert gas which properties are tabulated. The experiment ranges from high pressure where the flow is of laminar Stokes-type presenting slippage, down to very low pressures where the flow is molecular. In the molecular regime, when the mean-free-path is of the order of the distance between the suspended nano-mechanical probe and the bottom of the trench we resolve for the first time the signature of the boundary (Knudsen) layer onto the measured dissipation. Our results are discussed in the framework of the most recent theories investigating boundary effects in fluids (both analytic approaches and Monte-Carlo DSMC simulations).