Scanning tunneling microscopy and spectroscopy have been used to investigate the femtosecond dynamics of Dirac fermions in the topological insulator Bi$_2$Se$_3$ ultrathin films. At two-dimensional limit, bulk electrons becomes quantized and the quantization can be controlled by film thickness at single quintuple layer level. By studying the spatial decay of standing waves (quasiparticle interference patterns) off steps, we measure directly the energy and film thickness dependence of phase relaxation length $l_{phi}$ and inelastic scattering lifetime $tau$ of topological surface-state electrons. We find that $tau$ exhibits a remarkable $(E-E_F)^{-2}$ energy dependence and increases with film thickness. We show that the features revealed are typical for electron-electron scattering between surface and bulk states.