using System;
using System.Collections.Generic;
using System.Linq;
using System.Text;

namespace ConsoleApplication1
{
    class Program
    {
        static void Main(string[] args)
        {
            byte[] arr = { 0xFA, 0xAF, 0x00, 0x03, 0x00, 0x31, 0x31, 0x33, 0xFA, 0xAF, 0x00, 0x02, 0x00, 0x34, 0x35 };
            List<int> toRemove = new List<int>() { };
            bool fa = false;
            for (int i = 0; i < arr.Length; i++)
            {
                if (arr[i] == 0xFA) { fa = true; continue; }
                if (arr[i] == 0xAF && fa) { toRemove.AddRange(Enumerable.Range(i - 1, 5)); i += 3; fa = false; };
            }
            arr = arr.Select((x, i) => new { x, i }).Where(x => !toRemove.Contains(x.i)).Select(x => x.x).ToArray();
            Console.WriteLine(string.Join(" ", arr.Select(x => x.ToString("X2"))));
        }
    }
}

你这串数据主要应用于什么场景的？如果是通讯场景，这么用不合适会有大量内存碎片，建议遍历一次，查出并保存FA,AF开头的索引号，通过索引号数量知道了新字符串长度，new byte[]相应长度的数组，再使用Buffer.BlockCopy复制进新数组

31 31 33 34 35
Press any key to continue . . .