Looks like ClearTable is not the correct method. As per the code, its doing

ClassMethod %ClearTable(pTable As %String)
{
Kill ^Ens.LookupTable(pTable)
}

so..i did this but not too comfortable touching the globals directly. Hoping there is a cleaner way... (the below works)..

Table initialization

s tmpTable = ##class(Ens.Util.LookupTable).%New()
s ^Ens.LookupTable("myNiCTmpTable00992314","DUMMYVAL")=0 //create some randomly named table

<....use this tmp table for lookup and adding new rows.>

delete the tmpTable once done with usage

d tmpTable.%ClearTable("myNiCTmpTable00992314")

Edit: Adding a 2 digit random number at the end of the temp table name to ensure no conflict if multiple threads are running at the same time.