using System;

using System.Collections.Generic;

using System.Linq;

using Newtonsoft.Json;

using Newtonsoft.Json.Linq;

public class Program

{

    public static void Main()

    {

        string json_string = @"{

            ""Class 1"" : [

            {

                ""Key1"": ""value1"",

                ""Key2"": ""value3""

            },

            {

                ""Key3"": ""value3"",

                ""Key4"": ""value4""

            }

            ],

            ""Class 2"" : [

            {

                ""Key11"": ""value11"",

                ""Key21"": ""value31""

            },

            {

                ""Key31"": ""value31"",

                ""Key41"": ""value41""

            }

            ],

            ""Class 3"" : [

            {

                ""Key112"": ""value112"",

                ""Key212"": ""value312""

            },

            {

                ""Key312"": ""value312"",

                ""Key412"": ""value412""

            }

            ],

            ""Class 4"" : [

            {

                ""Key12"": ""value12"",

                ""Key22"": ""value32""

            },

            {

                ""Key32"": ""value32"",

                ""Key42"": ""value42""

            },

            {

                ""Key321"": ""value321"",

                ""Key421"": ""value421""

            }

            ]

        }";

        List<string> remainedKeys = new List<string> { "Class 2", "Class 4" };

        //var jsonObj = JObject.Parse(json_string).ToObject<Dictionary<string, List<dynamic>>>();

        var result = JObject.Parse(json_string)

            .ToObject<Dictionary<string, List<dynamic>>>()

            .Where(x => remainedKeys.Contains(x.Key))

            .ToDictionary(x => x.Key, x => x.Value);

        Console.WriteLine(JsonConvert.SerializeObject(result));

    }

}

​

​