Seriously, there are no computer programs that are capable of performing 3D reconstruction. There are only experimental applications that are limited to small and well behaved universes.
This is a list of software (both commercial and otherwise) available for 3D reconstruction of MRI, CT, confocal, and serial-section data for medical/life-sciences imaging.
3-D-E
Windows-based contour editor and visualizer from Data Cell Ltd. (Platforms: PC; Cost: ~$1500)
3-D-E Visualiser and Contour Editor 3-D-E, supplied by Data Cell, is a Windows based software product designed to take 2D image data and reconstruct to a 3-D surface rendered object. It allows the user to view, rotate and zoom under mouse control in real time on a 486 PC.
You do have very efficient and reliable free software doing 3D reconstruction.
-For cross section picture (like CT-scan I presume), you have Fiji (a package of ImageJ) will do the job. Follow the short video for more information about that:
https://www.youtube.com/watch?v=2N7i_gGYGLQ
-For 3D reconstruction with "normal" picture, you have free software such as 123D catch or Memento Beta both from Autodesk.
http://www.123dapp.com/catch
https://memento.autodesk.com/about
However keep in mind the 3D reconstruction highly depend on the quality of the pictures. Please follow the page to learn more about:
Personally I use Memento Beta and about 200 to 250 pictures for 3D reconstruction. Keep also in mind that the accuracy is about few millimetre to 1 cm.
Try Tomopy. It is free, versatile, and very powerful. You can download the source files here http://tomopy.github.io/tomopy/install.html . But there are a lot of external dependencies you need to download. I recommend installing with Anaconda, which is a program that tracks down, downloads, and configures all the external dependencies needed to run a software. Download here: http://continuum.io/downloads . If you are using Linux or OS X, type "conda install -c dgursoy tomopy" in the terminal to install.