I have 40 rows in Excel starting with a SerialID in sheet 1. In sheet 2 i have 109 rows which I would like to filter based on sheet 1. Sheet 1 contains records i want to hide from sheet 2.

Assuming the SerialIDs are in ColumnA of each sheet, add a column in sheet 2 with a formula of the kind =VLOOKUP(A2,Sheet1!A:A,1,FALSE) (adjust A2 as required) and copy down. This should find those that exist in sheet 1 so filter to select those that don't (ie tick #N/A only).