In the last decade, structural health monitoring (SHM) systems became essential to accurately monitor structural response due to real-time loading conditions, detect damage in the structure, and report the location and nature of this damage. Spectral analysis using Fourier transform has been widely used in SHM. In this research, a novel approach for the characterization of in structure damage in civil structure is introduced. The target is to develop vibration-based damage detection algorithms that can relate structural dynamics changes to damage occurrence in a structure. This article presents a new method utilizing high resolution spectral analysis based on Fast Orthogonal Search (FOS) techniques. FOS is a signal processing tool developed to provide high-resolution spectral estimation. In addition, it is a general-purpose non-linear modeling technique that finds functional expansions using an arbitrary set of non-orthogonal candidate functions. In order to examine the proposed method, the IASC-ASCE structural health monitoring benchmark structure is used in this study to illustrate the merits and limitation of the proposed approach. We also discuss the merits and the limitations of FOS as applied to SHM.