There's a couple of things you can do:
1) At search time you can add the following (assuming it's your host field that contains the fully qualified domain name):
<base_search>
| rex field=host "^(?P<hostname>[^\.]+)"
| eval hostname=lower(hostname)
Then you can use the new field "hostname" to do your check against your lookup.
2) Otherwise you can define a "calculated field" to extract the value out of the fully qualified domain name field:
lower(mvindex(split(host,"."),0))
This assumes that your FQDN is stored under field 'host', and it will grab everything up to the first period as the value for whatever field you define.
Hope this helps
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