When i read your title, i thought you were asking for a tool like Sketch UP , where you can create (not make) a software and then load it on a viewer (ViewUP) elsewhere.
How can i make a software that load 3d object and can manipulate it?
Looking at your explanation, I think your question is about individual graphics formats like Maya, and how to create a 3d Modelling tool (a basic version).
You need to do a bit of research on existing (open) 3d format. From what i just now searched 3d 'standards' are a diverse topic in itself.
If you are aiming to create something for a college project or a simple prototype , i would urge you to look at WebGL.
Note - For practical purposes, nobody would want to create their own 3D modelling tool, because of the sheer amount of work it is, and the commercials cannot justify it when there are excellent 3d modelling tools ( freeware and proprietary) available to do the job for you.
3D modelling tools are not developed by individuals but institutions that also play a significant role in defining the computing standards based on industry requirements, which has paved the way for the development of industry specific modelling and simulation environments, ( Simulink, Matlab, AutoDesk Maya, 3DStudio Max, Blender and many others) offering 3d modelling capabilities.
Developing a full fledged 3D modelling tool requires a comprehensive understanding of GPU programming and OpenGL ( the hardware implemented state machine) that all Graphic APIs use to create graphics, particularly 3d.
You should also take a look at this brief on CUDA, and the associated docs for GPU programming.
There are higher level libraries that one can use to generate 3d Graphics .
Learn Open GL is my favourite site to introduce beginners to the subject.