The # tag will come by default in Informatica. If you want to remove the # from the target file header you can do that in one of the below ways,
1) By using Unix Script.
2) Use custom header option available in Informatica and override the customized header as per your need.
Go to session target property and override/change the option as per below,
Use header command output
echo “header 1, header 2”
Hope this clarifies your question!