Hey, filebeat.inputs reads two log files. I am sending it to elasticsearch How can I show them in two different index names in kibana?

You can send to different indices based on any of the fields present in the document, so you could do something like the below:

output.elasticsearch:
  index: "default-%{+yyyy.MM.dd}"
  indices:
    - index: "application-one-%{+yyyy.MM.dd}"
      when.equals:
        application: "one"
    - index: "application-two-%{+yyyy.MM.dd}"
      when.equals:
        application: "two"

Would this work for you?

You can also cut out the middle man on the above and do something like:

output.elasticsearch:
  index: "%{[my-application-field]}-%{+yyyy.MM.dd}"