I am working with Stanford CoreNLP and using it for NER. But when I extract organization names, I see that each word is tagged with the annotation. So, if the entity is \"NE
No, CoreNLP 3.5.0 has no utility to merge the NER labels. The next release (coming sometime next week) has a new MentionsAnnotator which handles this merging for you. For now, you can (a) use the MentionsAnnotator, available on the CoreNLP master branch, or (b) merge manually.
Use the -outputFormat xml option to have CoreNLP output XML. (Is this what you want?)