Alfven eigenmodes driven by energetic particles are routinely observed in tokamak plasmas. These modes consist of poloidal harmonics of shear Alfven waves coupled by inhomogeneity in the magnetic field. Further coupling is introduced by 3D inhomogeneities in the ion density during the assimilation of injected pellets. This additional coupling modifies the Alfven continuum and discrete eigenmode spectrum. The frequencies of Alfven eigenmodes drop dramatically when a pellet is injected in JET. From these observations, information about the changes in the ion density caused by a pellet can be inferred. To use Alfven eigenmodes for MHD spectroscopy of pellet injected plasmas, the 3D MILD codes Stellgap and AE3D were generalised to incorporate 3D density profiles. A model for the expansion of the ionised pellet plasmoid along a magnetic field line was derived from the fluid equations. Thereby, the time evolution of the Alfven eigenfrequency is reproduced. By comparing the numerical frequency drop of a toroidal Alfven eigenmode (TAE) to experimental observations, the initial ion density of a cigar-shaped ablation region of length 4cm is estimated to be n() = 6.8 x 10(22) m(-3) at the TAE location (r/a approximate to 0.75). The frequency sweeping of an Alfven eigenmode ends when the ion density homogenises poloidally. Modelling suggests that the time for poloidal homogenisation of the ion density at the TAE position is tau(h) = 18 +/- 4 ms for inboard pellet injection, and tau(h) = 26 +/- 2 ms for outboard pellet injection. By reproducing the frequency evolution of the elliptical Alfven eigemnode (EAE), the initial ion density at the EAE location (r/a approximate to 0.9) can be estimated to be n() = 4.8 x 10(22) m(-3). Poloidal homogenisation of the ion density takes 2.7 times longer at the EAE location than at the TAE location for both inboard and outboard pellet injection.