using System;

using System.Linq;

using System.Collections.Generic;

public class Program

{

    public static void Main()

    {

        string input = "Net Sales,COGS";

        string[] values = { "Net Sales", "COGS", "COGS%", "Gross Profit", "GP%", "Quantity" };

        var result = FilterArray(values, input.Split(','));

        result.FilteredArray.Dump();

        result.IndexesOfRemainingElements.Dump();

    }

    static Result FilterArray(string[] array, string[] input)

    {

        var remainingElements = array.Where(i => !input.Contains(i)).ToArray();

        return new Result(remainingElements, 

                          remainingElements.Select(i => Array.IndexOf(array, i)).ToList());

    }

}

​

public struct Result

{

    public readonly string[] FilteredArray;

    public readonly List<int> IndexesOfRemainingElements;

    public Result(string[] filteredArray, List<int> indexesOfRemainingElements)

    {

        FilteredArray = filteredArray;

        IndexesOfRemainingElements = indexesOfRemainingElements;

    }

}