I am currently working on an ASP.NET 3.5 and C# web application which deals with users private information like SSN numbers. What are some of the security measures which I need to take from an application development stand point to feel safe?
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To secure your application you will need to understand the threats it will face and then develop appropriate mitigation techniques. A good place to start would be by creating a threat model.
Have a look at some of these resources: