By putting different chips on the same mask, shuttle mask (or multiple project wafer) provides an economical solution for low volume designs and design prototypes to share the rising mask cost. A challenging floorplanning problem is to optimally pack these chips according to objectives and constraints related to cost and manufacturability. In this paper, we study the problem of CMP aware shuttle mask floorplanning, which is formulated as a rectangle packing problem with objectives of area and post-CMP topography variation minimization. We propose a 3-step procedure to solve the problem. First, we use the low-pass filter oxide CMP model to guide the simulated annealing search to minimize the topography variation. The result is then further improved by sliding each chip in its enclosing rectangle. Finally, we calculate the optimal amount of dummy feature needed with a linear programming method. Our experiment shows excellent results on real industry data.