In ElasticSearch, how do I filter the nested documents in my result?

hits section returns a _source - this is exactly the same document you have indexed.

You are right, nested query filters top-level results, but with inner_hits it will show you which inner nested objects caused these top-level documents to be returned, and this is exactly what you need.

names field can be excluded from top-level hits using _source parameter.

{
   "_source": {
      "excludes": ["names"]
   },
   "query":{
      "bool":{
         "must":[
            {
               "term":{
                  "number":{
                     "value":"1234"
                  }
               }
            },
            {
               "nested":{
                  "path":"names",
                  "query":{
                     "term":{
                        "names.lastName":"Jones"
                     }
                  },
                  "inner_hits":{
                  }
               }
            }
         ]
      }
   }
}

So now top-level documents are returned without names field, and you have an additional inner_hits section with the names that match.
You should treat nested objects as part of a top-level document. If you really need them to be separate - consider parent/child relations.

Try something like this

{
   "query": {
      "filtered": {
         "query": {
            "match_all": {}
         },
         "filter": {
            "bool": {
               "must": [
                  {
                     { "term": { "number":1234} }
                  },
                  {
                     "nested": {
                        "path": "something",
                        "query": {
                           "term": {
                              "something.lastName": "Jones"
                           }
                        },
                        "inner_hits" : {}
                     }
                  }
               ]
            }
         }
      }
   }
}

I used this Refrence