When you save your file, you can use a program to crop it. Even default Preview has got this option (you select the area and use Command + K keys to crop it).

But there is even a better solution. You can screenshot only the parts of the screen you want. Please have a look at the screen below where you will find two shortcuts to use.

After selecting the keys, I use Shift + Command Key + 4, you select the part of the screen you want to save and the only these parts are captured. I hope this will help, please let me know if you have other questions regarding this topic.