[quote user="Mohammad Aryafar"]I found it very confusing using it as the most simple example (basic) uses multiple files[/quote]
The basic example is not the simplest. It demonstrates an elementary user interface (UI), and so adds resource files to the project that define the UI. Many examples include a command table, which again adds a resource file and more steps to the build process. I don't think that there are many MDL example projects that have no resource files and would therefore be the simplest for you to tackle first (your version of MicroStation is over ten years old, and my brain can't teleport me back that far).
You might like to start with a C project outside MicroStation. Get hold of a freeware C compiler and linker and build some simple command-line projects independent of MicroStation. Here are two references...
Don't use an IDE such as Visual Studio, because it hides the build steps and won't improve your understanding. When you've successfully built a plain old C app., it will become clearer to you what is the relationship between source code, intermediate files created during the build process, and the final app.
Next, move to bmake and an MDL project. The extra resource files used by MicroStation for UI, command tables, message lists and other things will be more obvious.