Filter by or with?

To choose either 'by' or 'with', you need to see if the phrase/word that comes next indicates a method or an instrument. If you want to show a method, you use by. If it's an instrument with which the activity was done, you use with:

• I opened the bottle by removing the cap

• I opened the bottle with a corkscrew

• I hit him by using a bat (the method is using something)

• I hit him with a bat

In your case, 'names' are a method used for filtering users list, not an instrument. So, you have to use 'by'. See the examples below:

I want to filter the users list by names

I want to filter the users list with a software that filters user lists by name