I need to create a template for sending email alerts in such a way that I can select columns for individual lists for the content to be displayed in the mail.
It's hard to know exactly how to answer based on the small amount of detail you have provided, but would a SharePoint Designer workflow serve the purpose? With that, you can set the text to whatever you'd like as well as include column values.
You can Create customtemplate for each type of library and can customize no of fields to be include/exclude.
Good example to go with CustomAlertTemplate.