The interaction of vortex filaments in an ideal incompressible fluid with the free surface of the latter is investigated in the canonical formalism. A Hamiltonian formulation of the equations of motion is given in terms of both canonical and noncanonical Poisson brackets. The relationship between these two approaches is analyzed. The Lagrangian of the system and the Poisson brackets are obtained in terms of vortex lines, making it possible to study the dynamics of thin vortex filaments with allowance for finite thickness of the filaments. For two-dimensional flows exact equations of motion describing the interaction of point vortices and surface waves are derived by transformation to conformal variables. Asymptotic steady-state solutions are found for a vortex moving at a velocity lower than the minimum phase velocity of surface waves. It is found that discrete coupled states of surface waves above a vortex are possible by virtue of the inhomogeneous Doppler effect. At velocities higher than the minimum phase velocity the buoyant rise of a vortex as a result of Cherenkov radiation is described in the semiclassical limit. The instability of a vortex filament against three-dimensional kink perturbations due to interaction with the "image" vortex is demonstrated.