A continuum and molecular dynamics hybrid multiscale method is developed to simulate micro- and nano-fluid flows. The method uses the continuum Navier-Stokes equations for one flow region and atomistic molecular dynamics for another. The spatial coupling between continuum equations and molecular dynamics is achieved through constrained dynamics in an overlap region which can be obtained through finding the extremum of the integral of the Lagrangian under the constraint of velocity matching. To validate the numerical method, the proposed multiscale method is used to simulate sudden-start Couette flow and channel flow with nano-scale rough walls, showing quantitative agreement with results from analytical solutions and full molecular dynamics simulations for different parameter regimes. A hybrid numerical method is then used to study corner singularities in driven cavity flow. Continuum equations with no-slip boundary conditions predict singular stresses at the corners between moving and static walls. Molecular dynamics simulations are used to resolve these singular regions, and the flow field in the remainder of the cavity is obtained from the Navier-Stokes (NS) equation. This hybrid solution agrees well with fully atomistic simulations on small systems. The multiscale method allows five order of magnitude speed up in calculations on larger systems and is able to access length scales ranging from milimeter to single molecular when the multiscale method is combined with adaptive grid method. By comparing the hybrid solution to NS solutions at different Reynolds number, we show that slip occurs near the corners and that it can not be described by the Navier slip condition. At high wall velocities, the fluid also exhibits non-Newtonian behavior within five atomic diameters from the corner. The numerical algorithms pertinent to multiscale time and fast convergence to steady state flows will be presented. The applications of the proposed multiscale method for multiphase flows, thermal flows and electrokentic flows will be discussed.