This is a really tricky conversation to have because of all the philosophical baggage inherent in the question.
"do we know of any physiological processes that gives an individual control over thinking?"
How do you define individual? It's a very loaded term. And how do you define control? Libet's experiments suggest that there are deterministic processes in the brain that underlie decision making.
Anyway, with that in mind, it's a little understood process, but here is an example of a go at it:
Figure 1 includes a table of particular brain regions and associated behaviors.
But basically, you have an amygdala weighing the emotional significance of stimuli, a prediction of what will happen given particular choices (given the choices you're aware of) and some kind of optimization consideration that chooses the best option (in terms of short-term and/or long-term rewards). Different people at different times tend to focus either on short or long term.
For instance, one theory is that our frontal lobes project a lot of inhibitory connections to the rest of our brain and tend to weigh the consequences of actions. For some people though, their primal drives may be "stronger" so they're less likely to defer gratification and more likely to seek short-term rewards at the expense of long-term rewards.