I am looking for a good solution by which we can prevent an exe file to be uploaded on server.
It will be best if we can discard the upload by just reading the file headers as soon as we receive them rather than waiting for entire file to upload.
I have already implemented the extension check, looking for a better solution.
There is a how and a when/where part. The how is fairly simple, as binary files do contain a header and the header is fairly easy to strip out and check. For windows files, you can check the article Executable-File Header Format. Similar formats are used for other binary types, so you can determine types you allow and those you do not.
NOTE: Linked article is for full querying of the file. There are cheap, down and dirty, shortcuts where you only examine a few bytes.
The when/where depends on how you are getting the files. If you are using a highly abstracted methodology (upload library), which is fairly normal, you may have to stream the entire file before you can start querying the bits. Whether it is streamed into memory or you have to save and delete depends on your coding and possibly even the library. If you control the streaming up, you have the ability to stream in the first bytes (header portion) and abort the process in mid stream.
The first point of access to uploaded data would be in a HttpModule. Technically you can check before all the bytes are sent if you have an .exe on your hands and cancel the upload. It can get quite complicated depending on how far you want to take this.
I suggest you look at the HttpModule of Brettle's NeatUpload. Maybe it gives you a lead on how to deal with this on the level you want.
I think you can do that by a javascript by checking if the file end with .exe before submitting the data and also do the check server side.
MZ, odds are you've got an executable.