Should I say:
I want to filter users list by names.
I want to filter users list with names ??
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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