Starting a new scenario (our term for the application of MATSim to a region/area) can appear quite cumbersome at the first glace, as a lot of data preparation may be required. In any case required for a new scenario are:
Given these two data items, you can already start building your own scenario. The "Learning MATSim in 3 days"-Tutorial gives you an introduction on how to build your own scenario.
See here for javadoc, and here for code.
In many cases, using pre-configured software is not possible because there are just too many possibilities of how input could look like. Although matsim is not there yet, these should be api-only use cases, i.e. they should only use the "stable" api. Therefore, the following are under the api-users section of the documentation:
The following sections contains various information for building a scenario that presumably goes beyond what is in the tutorial.