Science tells us that thoughts are the activity of cells in our brains. Science also tell us that the activity of those cells has to have physical causes, because restrictions on physical possibilities imposed by the conservation of energy and momentum mean that there is no room for any other causes to have any direct influence on what happens in our brains.
So how do we get to have thoughts?
One is through the use of symbolic representation of abstractions combined with rules. We can work out that 2+2=4 because we have symbolic representations of numbers and we can mentally express the rule for adding.
The other way is through input from senses and memory. For example, we can get information from outside of our heads, such as from spoken words or things read. These inputs result in signals within our brains that we interpret based on evolved neural functions and on experience.
Another way is through the brain combining various combinations of memories together to form imagined situation and dreams.
The key thing to realise here is that these are all completely physical processes: every thought that arises arises because of underlying physical causes no matter what that thought may represent.
This means that no thought about any aspect of our minds being non-physical can be caused by that non-physical aspect - no thoughts or feelings about our minds can be used as evidence for non-physicality. We may have some experiences which we feel are beyond physical explanation, but we know from science that this feelings is deluding us, because all feelings must have physical explanations, otherwise we would not be able to think about them!