Expanding on my comment above, what I mean is you can use a search engine that can index your whole file system and then search for content.
An example of generic search engine I have used in the past is Sphinx Search. It has various plugins for different interfaces. There are others like Apache Solr, Elasticsearch, etc. They all require you to invest some time to undertsand how they work, and getting an interface e.g. a simple web page?
But to have a more structured search, you need a system like Calibre already suggested by others to import the pdfs...