The idea (for any system) is to start with understanding an adversary's perspective by:
- Listing application entry points (where does data enter into the application?)
- Cataloguing assets (what's being protected?)
- Identifying trust levels (who needs access to what?)
Then defining the security of the app/system by:
- Defining use scenarios
- Identifying implementation assumptions (parameter-based SQL?) and external dependencies (payment system?)
- Modelling the application/solution (data flow diagram that shows interactions with external entities, and machine and process boundaries)
The final stage is identifying threats, analysing them, and determining vulnerabilities. Threats typically fall into one of 6 categories:
- Spoofing
- Tampering
- Repudiation
- Information disclosure
- Denial of service
- Elevation of privilege
That stuff I've just written doesn't begin to do threat modelling justice, but it's enough to start some research.
And before anyone starts suggesting that it's not important/requires big design up front/we need to pivot/etc consider that exactly those arguments are what landed the likes of LinkedIn, Sony, etc. in hot water.