Measurements on vibrating structures has been a topic of interest for decades. Vibrating structures are however generally assumed to behave linearly and in a noise-free environment, which is not the case in practice. This paper provides a methodology that allows for the autonomous estimation of nonlinearities and assessment of uncertainties by bootstrap on a given vibrating structure. Nonlinearities are estimated by means of a block-oriented nonlinear model approach based on parallel Hammerstein models and on exponential sine sweeps. Estimation uncertainties are simultaneously assessed using repetitions of the input signal (multi-sine sweeps) as the input of a bootstrap procedure. Mathematical foundations and a practical implementation of the method are discussed using an experimental example. The experiment chosen here consists in exciting a steel plate under various boundary conditions with exponential sine sweeps and at different levels in order to assess the evolution of nonlinearities and uncertainties over a wide range of frequencies and input amplitudes.