In the following theoretical and numerically oriented work, a number of findings have been assembled. The newly devised VENUS-LEVIS code, designed to accurately solve the motion of energetic particles in the presence of 3D magnetic fields, relies on a non-canonical general coordinate Lagrangian formulation of the guiding-centre and full-orbit equations of motion. VENUS-LEVIS can switch between guiding-centre and full-orbit equations with minimal discrepancy at first order in Larmor radius by verifying the perpendicular variation of magnetic vector field, not only including gradients and curvature terms but also parallel currents and the shearing of field-lines. By virtue of a Fourier representation of the fields in poloidal and toroidal coordinates and a cubic spline in the radial variable, the order of the Runge-Kutta integrating scheme is preserved and convergence of Hamiltonian properties is obtained. This interpolation scheme is crucial to compute orbits over slowing-down times, as well as to mitigate the singularity of the magnetic axis in toroidal flux coordinate systems. Three-dimensional saturated MHD states are associated with many tokamak phenomena including snakes and LLMs in spherical or more conventional tokamaks, and are inherent to stellarator devices. The VMEC equilibrium code conveniently reproduces such 3D magnetic configurations. Slowing-down simulations of energetic ions from NBI predict off-axis deposition of particles during LLM MHD activity in hybrid-like plasmas of the MAST. Co-passing particles helically align in the opposite side of the plasma deformation, whereas counter-passing and trapped particles are less affected by the presence of a helical core. Qualitative agreement is found against experimental measurements of the neutron emission. Two opposing approaches to include RMPs in fast ion simulations are compared, one where the vacuum field caused by the RMP current coils is added to the axisymmetric MHD equilibrium, the other where the MHD equilibrium includes the plasma response within the 3D deformation of its flux-surfaces. The first model admits large regions of stochastic field-lines that penetrate the plasma without alteration. The second assumes nested flux-surfaces with a single magnetic axis, embedding the RMPs in a 3D saturated ideal MHD state but excluding stochastic field-lines within the last closed flux-surface. Simulations of fast ion populations from NBI are applied to MAST n=3 RMP coil configuration with 4 different activation patterns. At low beam energies, particle losses are dominated by parallel transport due to the stochasticity of the field-lines, whereas at higher energies, losses are accredited to the 3D structure of the perturbed plasma as well as drift resonances.