For Organic Chemistry, it is easy. Get an Organic Chemistry model kit and get into the habit of constructing three-dimensional models of the more complex molecules you are studying. When you see something written out, it's rather hard to "see," but after you construct a model you can rotate it in your hands and look at it from all angles. You can practice rotating it in your mind once you have the model sitting in front of you. Once you've done this a bunch of times with different molecules, you'll be able to mentally create the three-dimensional models and translate the written out forms into the actual equivalents. I came up with some neat tricks using models to help me solve organic chemistry test questions quickly, without using models.
For physics, practice it in your mind. You can also draw pictures. I once saw a Physics graduate student, who was going over our homework problems, solve a really difficult question almost just by drawing out a clear picture of what the question was stating. The solution almost followed just from the picture. I was really amazed at what making a clear diagram can do.
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