This invention provides a system and method that performs 3D imaging of a complex object, where image data is likely lost. Available 3D image data, in combination with an absence/loss of image data, allows computation of x, y and z dimensions. Absence/loss of data is assumed to be just another type of image data, and represents the presence of something that has prevented accurate data from being generated in the subject image. Segments of data can be connected to areas of absent data and generate a maximum bounding box. The shadow that this object generates can be represented as negative or missing data, but is not representative of the physical object. The height from the positive data, the object shadow size based on that height, the location in the FOV, and the ray angles that generate the images, are estimated and the object shadow size is removed from the result.