While signal estimation under random amplitudes, phase shifts, and additive noise is studied frequently, the problem of estimating a deterministic signal under random time-warpings has been relatively unexplored. We present a novel framework for estimating the unknown signal that utilizes the action of the warping group to form an equivalence relation between signals. First, we derive an estimator for the equivalence class of the unknown signal using the notion of Karcher mean on the quotient space of equivalence classes. This step requires the use of Fisher-Rao Riemannian metric and a square-root representation of signals to enable computations of distances and means under this metric. Then, we define a notion of the center of a class and show that the center of the estimated class is a consistent estimator of the underlying unknown signal. This estimation algorithm has many applications: (1)registration/alignment of functional data, (2) separation of phase/amplitude components of functional data, (3) joint demodulation and carrier estimation, and (4) sparse modeling of functional data. Here we demonstrate only (1) and (2): Given signals are temporally aligned using nonlinear warpings and, thus, separated into their phase and amplitude components. The proposed method for signal alignment is shown to have state of the art performance using Berkeley growth, handwritten signatures, and neuroscience spike train data.