There are three levels in every thought and judgment.
Recognition. “This is a cup, this is a book, this is a car crash”. The first step comes from our animal nature. Our brain recognizes things automatically and sends us a signal. We don’t control this part.
Automatic judgment. Our brain records the event and instantly gives it a judgment. Someone is screaming at you? Be scared, get aggressive, protect yourself. Run, attack. This is also part of our animal nature and partly under our control. We can change our judging mechanism here by having better value-judgments. Changing your behavior here takes a long time and requires a deep restructuring of our value system. Even the Stoic sage gets scared for a second when someone opens fire next to him.
Rationality. Higher spirit. Guiding principle. This is the rational part of your brain that sees step 1 and step 2 happening from the side and puts the event into context and rationalizes it. This is completely under our control. We can see the event clearly with our rational mind and can decide to either follow our animal nature and panic, run, or attack. Or we can change our reaction when it’s not according to our principles. This is where the real work of becoming better happens. Seeing the automatic labels that our brain puts on things and re-labeling them according to our principles. Do this over and over again and you see yourself transform.
I’ve sometimes found it discouraging to see myself automatically judging many things in a way I would never do “myself” rationally. Is this my “real self” doing it? I guess it is, in some way. It’s “myself” as the animal doing that. It’s “myself” as the kid that grew up in a modern society with the wrong principles doing it.
Don't get discouraged. Understand that you are only in control of your rational self. Don't worry about not having “the correct” animal nature, I assume nobody does. Make sure you make the right choices and give things the correct labels in Step number 3. Over time, you will also see your value-judgments change, and labeling things correctly will become more automatic.
Paint your soul with the color of your thoughts.