Which is correct?
- I am writing to apply for the position of ____ in your company.
- I am writinng to apply for the position of ____ at your company.
- I am writinng to apply for the position of ____ for your company.
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As part of my job as an project manager, I have written a few job descriptions and read quite a few inquires like the one you mention. In my experience, when the phrase is "work --- your company", it is almost always "at your company". Actually, it is usually phrased "at Acme Widgets" or whatever the company name is.
If the company pays you, you work for the company. Most people would also work at the company. An exception, as Mamta D says, is that consultants don't work at the company. In American English, people don't work in a company--they work in a specific department such as accounting. They also work in a specific building and at a specific location (street address).
Although people work for a company, the job is not for the company, it is at the company. So, you could apply to be an accountant for Acme Widgets, apply to work in the accounting department at Acme Widgets or apply for the position of accountant at Acme Widgets. The third form is what I most often see.