How to filter system query from DMV ?

What do you mean by system query? Is it you want to have a database specific query?

How do you know if a use is executing a query contains system tables?

If you want to get the queries getting executed NOT on a system databases, then below would help you.

SELECT TOP 50
    TextData           = qt.text
    ,DiskReads          = qs.total_physical_reads   -- The worst reads, disk reads
    ,MemoryReads        = qs.total_logical_reads    --Logical Reads are memory reads
    ,Executions         = qs.execution_count
    ,TotalCPUTime       = qs.total_worker_time
    ,AverageCPUTime     = qs.total_worker_time/qs.execution_count
    ,DiskWaitAndCPUTime = qs.total_elapsed_time
    ,MemoryWrites       = qs.max_logical_writes
    ,DateCached         = qs.creation_time
    ,DatabaseName       = DB_Name(qt.dbid)
    ,LastExecutionTime  = qs.last_execution_time,*
 FROM sys.dm_exec_query_stats AS qs
 CROSS APPLY sys.dm_exec_sql_text(qs.sql_handle) AS qt
 where DB_Name(qt.dbid) not in ('msdb','master','tempdb','model','resource') Or DB_Name(qt.dbid) is null
 ORDER BY qs.total_worker_time DESC