In general, flying vehicles which shear through air are subjected to various types of worst environmental loads. The components such as wing, vertical tail, booster fins were been heavily subjected to aerodynamic loads. As these components are designed for minimum weight configuration that results in very flexible structures, which leads to various types of structural interaction problems like flutter, divergence and so on. Hence every aerospace vehicle and its components should be analysed for its aeroelastic problems. The first part of the paper explains the methodology adopted for carrying out the flutter analysis using CAE. The latter part discusses the flutter analysis of the substructure or the component level, in the interface fixed condition. This substructure level flutter analysis is important during the preliminary design phase. Once the component clears the flutter margin, then the FEM of the componenets are assembled to form the Global model of the space vehicle. The flutter analysis of the space vehicle is carried out in free-flight condition because the structural dynamics of the vehicle is completely different form the substructure level. The doublet lattice, zona51 and piston theories are used in the unsteady aerodynamic calculations for the speed regimes subsonic, supersonic and hypersonic. As there is no theoretical procedure for transonic speeds, doublet lattice method has been used in the present analysis. The flutter analysis is carried out for various mach numbers and identifying the flutter instability of the space vehicle for various Mach numbers. Frequency (ω) and damping (ξ) versus velocity are presented to identify the flutter velocities and the flutter behavior.