In this paper, a novel reconstruction method based on free-form deformation (FFD) and External Axes Projection (EAP) is presented to improve the surface smoothness effect of 3D reconstruction. The contours of the slices are implicitly embedded in a higher dimensional space of distance transforms. In this implicit embedding space, reconstruction is formulated as follows. First, an arrangement of the planar slices is computed to support the approach. The arrangement consists of cells, and each cell consists of two adjacent contours. Second, the branching problem is converted into one-to-one case by the external axes projection. Next, computing direction for each cell of the arrangement is decided by the length energy. Then, in each cell a B-spline based free-form deformation is used to establish the correspondence between the adjacent contours. Finally, the contours are stitched together based on the correspondence. The key advantage of such framework are:(1) it naturally deals with contours of arbitrary topology, and it preserves shape topology; (2) the established one-to-one correspondences between two adjacent contours can guarantee the surface is continuous and no intersection; and (3) this framework is highly parallel. Experimental results show that the proposed approach performs well and can handle complicated situations.