The Filter stopwords setting enables or disables the stopword filtering. Stopwords are words that usually do not contribute as classification features. Usually stopwords are high frequency words like articles, connectors, etc.
Stopwords are selected from a predefined set of words that depends on the language you have chosen. If you selected Other / Multi-language stopwords won’t be filtered.
If you want to override the default stopwords for your language or particular case you can add here a list of comma separated stopwords that will be ignored. This feature is useful when you find that some wrong keywords are used as features in the classifier (by looking at the keyword cloud). In that case, you can filter them by adding them to the list of stopwords.