Software

There are three main approaches to producing 3D forms with software:

Polygonal - Points in 3D space, called vertices, are connected by line segments to form a polygon mesh. These types of models are very fast for computers to render, so are most commonly used for games, special effects and animation. They are however only approximate in there rendering, so they are not suitable for highly detailed product design or engineering.
Curve or NURBS - Surfaces are defined by curves based on mathematics models. NURBS based software can produce highly accurate models, that can be scaled indefinitely
Digital sculpting or volumetric modeling. Voxel(3D pixels) based modelling are less common but off some unique advantages by representing volume in a form. It's commonly used for digital clay applications and for 3D printing material composites.

Modeling / Scripting (CAD

processing (P3D, dxf export, peasycam, controlp5, toxiclips) https://processing.org/download/
https://tinkercad.com (web app, no need to download) (web app, no download)
Meshmixer
www.meshmixer.com/
Onshape https://www.onshape.com/ (Optional)

3D Scanning

Preparing Fabrication

Meshlab (http://meshlab.sourceforge.net/)
As you want to print in 3D you need to clean up (close) the shapes. Meshlabs fixes holes and overlappings.

Fabrication (CAM