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My init.vim code:

autocmd BufNewFile *.cpp 0r C:\Users\User\Desktop\cp\Template.cpp

When i create a .cpp file, Template.cpp code is imported in that cpp file.
upto this point, everything is fine.

but while doing that, vim always leaves a last blank line (which i don't want)

#include <iostream>
using namespace std;

int main(){
    // code goes here
}
-- unwanted last line --

So can anyone help me fix this problem?

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:r inserts the contents of a file. It does not overwrite existing contents. Since a new file opened in Vim can't have zero lines* you'll be adding the file's contents to one blank line.

Simplest thing to do is just add an additional command to your autocommand:

autocmd BufNewFile *.cpp 0r C:\Users\User\Desktop\cp\Template.cpp | $d

So we use | to indicate an additional command and :d[elete] with a "range" of $ (last line).

Or, if you'd prefer to start with the cursor at the beginning of the buffer:

autocmd BufNewFile *.cpp r C:\Users\User\Desktop\cp\Template.cpp | 1d

* According to various definitions/specifications (including POSIX) a "text file" must contain at a minimum a terminating line feed character. IOW, totally empty files are not considered text files and Vim is a text file editor...

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