SQL Server Query Performance Issue: Need Replacement of NOT EXISTS - sql

Question

Could someone optimitize the performance of below General SQL Query:
select fn.column1
from dbo.function1(input1) as fn
where (not exists (select 1 from table1 t1
where fn.column1 = t1.column1)
and not exists (select 1 from table2 t2
where fn.column1 = t2.column1))
For the above query, consider the approximate row count given below.
select fn.column1 from dbo.function1(input1) as fn -- returns 64000 records in 2 seconds.
table 1 (Column1) record-- returns 3000 records -- 1 second
table 2 (Column1) record-- returns 2000 records -- 1 second
So, if I run each select statement, it pulls and displays record in 1 or 2 seconds. But, if I run the full query, it takes more than a minute to display 64000 - (3000 + 2000) = 59000 records.
I tried the using EXCEPT like this:
select fn.column1
from dbo.function1(input1)
except
(select column1 from dbo.table1 union select column1 from dbo.table2)
Nothing improves my performance. Same it takes a minute to display 59000 records. This is with the same case for "NOT IN" Scenario.
Also I noticed that if we use UNION, instead of EXCEPT in the above query, it returns 59K records in 2 seconds.
UPDATED:
The function (a bit complex) contains the below pseudocode
select column1, column2,...column6
from dbo.table1
inner join dbo.table2
inner join ....
inner join dbo.table6
inner join dbo.innerfunction1
where <Condition 1>
UNION ALL
select column1, column2,...column6
from dbo.table1
inner join dbo.table2
inner join ...
inner join dbo.table4
inner join dbo.innerfunction2
where (condition 2)
Assume that two inner functions has single table select statement
My question is: if I select the column from the function, it displays 64K records in 1 sec. But, if the whole query executed, it takes more than a minute.
[Please Note: This query need to be used in function]
Could any one help me to improve this?
Kindly let me know if you need more details or clarifications.
Regards,
Viswa V.

Answer 1

Its a bit hard to optimize without data to play with. A fiddle would be good. Nonetheless here is an approach that may work.
Create a temp table, index it then do the EXCEPT as follows:
SELECT
fn.column1
INTO
#temp
FROM
dbo.function1(input1) AS fn
CREATE NONCLUSTERED INDEX [temp_index] ON #temp
(
column1 ASC
)
SELECT
column1
FROM
#temp AS t
EXCEPT
(
SELECT
column1
FROM
dbo.table1
UNION
SELECT
column1
FROM
dbo.table2
)
I would be interested in the result.