How to define seperated indexes for different logs in Filebeat/ELK?

In your Filebeat configuration you can use document_type to identify the different logs that you have. Then inside of Logstash you can set the value of the type field to control the destination index.

However before you separate your logs into different indices you should consider leaving them in a single index and using either type or some custom field to distinguish between log types. See index vs type.

Example Filebeat prospector config:

filebeat:
  prospectors:
    - paths:
        - /var/log/redis/*.log
      document_type: redis

    - paths:
        - /var/log/python/*.log
      document_type: python

    - paths:
        - /var/log/mongodb/*.log
      document_type: mongodb

Example Logstash config:

input {
  beats {
    port => 5044
  }
}

output {
  # Customize elasticsearch output for Filebeat.
  if [@metadata][beat] == "filebeat" {
    elasticsearch {
      hosts => "localhost:9200"
      manage_template => false
      # Use the Filebeat document_type value for the Elasticsearch index name.
      index => "%{[@metadata][type]}-%{+YYYY.MM.dd}"
      document_type => "log"
    }
  }
}

filebeat.yml

filebeat.prospectors:

- input_type: log
    paths:
    - /var/log/*.log
  fields: {log_type: toolsmessage}


- input_type: log
  paths:
    - /etc/httpd/logs/ssl_access_*
  fields: {log_type: toolsaccess}

in the logstash.conf.

input {
  beats {
    port => "5043"
  }
}

filter {
  if ([fields][log_type] == "toolsmessage") {
    mutate {
      replace => {
        "[type]" => "toolsmessage"
      }
    }
  }
  else if ([fields][log_type] == "toolsaccess") {
    mutate {
      replace => {
        "[type]" => "toolsaccess"
      }
    }
  }
}

output {
  elasticsearch {
    hosts => ["10.111.119.211:9200"]
    index => "%{type}_index"
  }
 #stdout { codec => rubydebug }
}