Asp.net deploy - file Main.Master.cs not found

I am currently hosting my site on the azure. One of my pages is working fine, but I have another page that uses the main page, which does not load, because I get this error:

Server Error in '/' Application.

Parser Error

Description: An error occurred during the parsing of a resource required to service this request. Please review the following specific parse error details and modify your source file appropriately. 

Parser Error Message: The file '/Main.master.cs' does not exist.

Source Error: 


Line 1:  <%@ Master Language="C#" AutoEventWireup="true" CodeFile="Main.master.cs" Inherits="ThirdEye.Main" %>
Line 2:  
Line 3:  <%@ Register Src="~/controls/Footer.ascx" TagName="Footer" TagPrefix="ThirdEye" %>

Source File: /Main.master    Line: 1 

Version Information: Microsoft .NET Framework Version:4.0.30319; ASP.NET Version:4.0.30319.272

I can’t understand what’s wrong with me. I downloaded the executable file, the pages are in the same directory of the bin folder. Do you think I need to add a period or tilde in front of the CodeFile or Inherits attribute?

I am using .net framework v4. I can't use 3.5, and I don't think this should be a problem.

Main.Master

<%@ Master Language="C#" AutoEventWireup="true" CodeFile="Main.master.cs" Inherits="Main" %>

Main.Master.cs

using System;
using System.Collections.Generic;
using System.Linq;
using System.Web;
using System.Web.UI;
using System.Web.UI.WebControls;
using System.Web.UI.HtmlControls;
using ThirdEye;

public partial class Main : System.Web.UI.MasterPage
    {....