A method of and a system for extracting 3D bag images from continuously reconstructed 2D image slices are provided. The method detects the boundaries of baggage in the reconstructed images, and provides better flexibilities for threat detection and displaying. The method comprises detecting starting and ending slices using multiple slices, counting bag slices, splitting 3D bag images when maximum number of slices of a 3D bag image is reached, and creating overlapping slices for the split 3D bag images.