As @mfranz suggested, the Overlapping Inventory Filter settings that @JJacildo mentioned are only helpful to filter out data when you have data for the same computer being imported from multiple sources - so that would help if the computers that are old in your SCCM database have current/new inventory being imported from another source (such as from the FlexNet inventory agent). It doesn't sound like this is your situation, so those settings are likely not helpful for you.
Best practice for dealing with old data is to deal with it at the source - i.e. in SCCM. Most organizations will have configuration in place in their SCCM system to delete/obsolete old inventory data after a period of time (such as 90 days). So consider talking to your SCCM team about whether they can put such a configuration in place in your environment.
If that isn't possible, another approach I've seen taken to address this sort of need is to set up a replica/duplicate copy of the SCCM database, and delete old/unwanted records from that copy before FlexNet Manager Suite reads data from it during its import process.
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