Hi mvaradarajam,
you cannot remove double quotes from output lookup csv file.
Splunk will put them around any values containing any non alphanumeric character. See this answer for more details http://answers.splunk.com/answers/114632/when-does-splunk-add-double-quotation-in-outputcsv.html
Anyhow, why is this a problem to you?
Can't you simply use something like this on the lookup fields:
... | head 1 | eval foo="\"quotes\"" | eval boo=trim(foo, "\"") | table foo boo
cheers, MuS