There are 2 main things:
1-Understanding the approach to make it MECE

2-Practice

To make your structure MECE, you should first think about what kind of answer would be a good answer for such a problem. Then you should think about how can you approach this question in a way that you reach this answer in the most practical way. This is what you do when you face with a math problem right, it is very similar.

This will give you an idea about the approach. Then try to jot down key items on your mind and check whether they are covering all area and these items are exclusive. If not, reiterate your approach. This is how we are defining the approach of large projects.

For the practice part, you can practice only structuring part of many cases. Then check the solutions and see why your approach was different, what was missing.

Hope it helps

Cheers

Serhat