The present work deals with the development and applications of least squares kinetic upwind method for moving nodes (LSKUM-MN). The LSKUM-MN is a meshfree solver capable of handling unsteady flow past multiple moving boundaries. The method originates from Least Squares Kinetic Upwind Method (LSKUM) which is a meshfree method. LSKUM formulation is modified to include the effect of moving nodes thereby leading to LSKUM-MN. Two step defect correction is generally used in LSKUM to achieve spatial higher order accuracy. In this work we have used MCIR splitting to achieve spatial accuracy. This avoids computing the moving fluxes for tertiary nodes if two step defect correction were used. Dual time stepping is used to achieve temporal accuracy. Eigen direction based weights are used to compute spatial derivatives which improves robustness of the code. This method has been applied to a variety of problems involving moving boundaries and unsteady flows. In this paper we present the application of the method to flow past multiple moving airfoils, flutter prediction in turbomachines and to time domain aeroelastic analysis. In flutter prediction problem we have used the energy method to determine flutter phenomenon. Strategy for movement of nodes is also critical in such computations. In time domain aeroelastic analysis we have used the Newmarks algorithm. 2-DOF model is used as structural model and LSKUM-MN serves the aerodynamic input. The flutter phenomenon for airfoil is studied using this approach.