It is sometimes easier to use one FKM for all servers even though they don't all contain the same files. This ensures uniformity in looks and makes it easier to create and maintain generic FKM rules and alerts.
In order to do this you could take the following two approaches:
1) Create an FKM sampler with no further configuration. For each managed entity or type you then configure a Sampler Include which lists the files that are required on this particular type of server. The empty FKM and Sampler Include combined will constitute a full FKM sampler.
2) Create one FKM sampler with all possible files listed. In the Visibility tab for the sampler, use a variable for hide rows. On each managed entity or type, define this variable as a StringList containing all the files you do not expect to see on this server.