If the message contains nested MSG files, to retain the nested MSG files as MSG files after import, select Extract nested messages > Import all attached emails as EML/MSG files option in the Import settings tab.

Sample code for using this feature.

using System;
using System.Collections.Generic;
using Kofax.KCS.ImportConnector.Config;
using Kofax.KCS.ImportConnector.Messages;
using Kofax.KCS.ImportConnector.Scripting;

namespace Kofax.KCS.ImportConnector.ScriptingSample
{
    /*
     * IDocumentConverterScript interface extends the functionality of IReRouteScript script.
     * IDocumentConverterScript exposes DocumentConverter() API along with ReRoute() API.
     * Using the implementation of IDocumentConverter interface in DocumentConverter() API, 
     * we can acheive the following functionality:
     * 1) Combine Body of a message with individual Attachments. (Check AppendBodyToAttachments_FR7043.cs in KCSImportScriptingSample.zip)
     * 2) Convert any Documents to PDF and/or Tiff. (Check SampleDocumentConverterScript.cs in KCSImportScriptingSample.zip)
     * 3) Concatenate individual PDFs to a single PDF/A document.(Check SampleDocumentCombineScript.cs in KCSImportScriptingSample.zip)
     * 4) Extract Zipped archives.(Check SampleUnzipScript.cs in KCSImportScriptingSample.zip)
     * */

    /// <summary>
    /// This sample script demonstrates the Document Conversion 
    /// functionality exposed by the interface IDocumentConverterScript
    /// </summary>
    public class SampleDocumentConverterScript : IDocumentConverterScript
    {
        /// <summary>
        /// This method is used to Convert dicuments to Tiff/PDF
        /// </summary>
        /// <param name="message">The message to be imported into KC</param>
        /// <param name="converter">The Document Converter Interface object</param>
        /// <returns></returns>
        public ConversionResult DocumentConverter(Message message, IDocumentConverter converter)
        {
            ConversionResult result = new ConversionResult();

            if (converter != null)
            {
                List<Attachment> convertedAttachments = null;
                List<Attachment> convertedAttachments1 = new List<Attachment>();
                DocumentConversionOptions options = new DocumentConversionOptions();

                /* ConversionDetails class exposes the following settings:
                 *  PDF Normalization
                 *  Flattening portfolio PDFs using Adobe Life Cycle
                 *  Image Quality
                 *  Image Resolution
                 *  Image Scaling and Image Coding
                 *  Smoothening and Rendering Flags
                */

                options.ConversionDetails = new ConversionDetails();

                // Configuring PDF Normalization and Flattening portfolio PDFs.
                options.ConversionDetails.isPdfNormalizationEnabled = true;
                options.ConversionDetails.isALCFlatteningEnabled = true;

                // To Convert documents to Tiff or PDF, configure the required options below.

                // Configuring PDF conversion.
                // NOTE: If the input is a PDF document, and PDF normalization is not enabled,
                // then output will be empty.
                //options.Pdf = 1;

                // Configuring Tif conversion.
                //options.Tif = 1;

                //Configuring Msg conversion.
                //For EML input only
                options.Msg = 1;

                //Configuring Msg conversion.
                //For MSG input only
                //options.Eml = 1;

                // Call the Convert API with the documents which needs conversion as input.
                foreach (Attachment att in message.BodyAttachments)
                {
                   if(att.Extension.ToLower()=="eml")
                   {
                     result = converter.Convert(out convertedAttachments, att, options);
                     if (result.Code == 0 && convertedAttachments != null && convertedAttachments.Count > 0)
                       {
                            // Add the converted documents to the message 
                            // so that they will be imported into Kofax Capture.
                            convertedAttachments1.AddRange(convertedAttachments);
                       }
                   }
                }
                if(convertedAttachments1 != null && convertedAttachments1.Count > 0)
                {
                    message.BodyAttachments.AddRange(convertedAttachments1);
                }
            }

            return result;
        }

        public eMessageScriptCode ReRoute(Message message, object extension)
        {
            return eMessageScriptCode.Other;
        }
    }
}

To enable this feature, do the following: