I have a scenario where i need to crete custom sharepoint service application and need to use FQL for getting the content from FAST and send the data to various farms or users through Email or someother process .Will it be possible to use custom sharepoint service application for FAST to get the content?
I really doubt that that is your scenarion. What you describe, is a solution for a specific problem and you are not sure that it is going to work. So my question for you:
what is your problem? Do you need to get always the same content? Or is it a static query that is always the same? Will you need to expose content to other applications than sharepoint in the future? What about seciurity trimming?
your first start will be to consume the web service that is tied to your site collection, to query your data by fql.
A custom service application is always possible, but I really doubt the need for it. Aside from that: custom service applications are a bit complex and do cost a lot of work, as you also need to implment UI, authorization etc. for it. maybe a small,reusable library will be sufficient for you.