1) You can filter folders when performing a migration within the Configuration Options -> Filter Options -> Folder name Filter
a. You can enter part of the name or the full name of the filter you wish to include. Entering part of the name will filter out ALL folders that have the text inputted as the name within the scope of the copy [Note Content Matrix uses inclusive filters and if you would like to exclude the folders from copying then you toggle the "Using as exclude filter" option]

2) If you'd like to filter more than one folder, and with different names then you'll have to utilize RegEx short for Regular Expressions
a. What will be required is to toggle the Configuration Option "Using regular expressions" and specify the criteria you want your regular expression to perform. For example, I have 2 different folders that are very large and I want to filter them out during my migration and migrate them at a later time. The Folders are subfolders, and they are called Test3Folder and FolderTest6. The RegEx criteria we will be specifying to filter them out is the following. (^Test3Folder$|^FolderTest6$)

3) Here is a link where you can find all information about Regular Expressions and ways to use them.
a. https://www.regular-expressions.info/