I don't know a tool that does this, but here is a piece of C++ code you can build that can change a DLL exported names. In this case, you can set the names you don't want to an empty string (the 0 character):

void RemoveUnwantedExports(PSTR ImageName)
{
    LOADED_IMAGE image;
    // load dll in memory for r/w access
    // you'll need Imagehlp.h and Imagehlp.lib to compile successfully
    if (MapAndLoad(ImageName, NULL, &image, TRUE, FALSE))
    {
        // get the export table
        ULONG size;
        PIMAGE_EXPORT_DIRECTORY exports = (PIMAGE_EXPORT_DIRECTORY)ImageDirectoryEntryToData(image.MappedAddress, FALSE, IMAGE_DIRECTORY_ENTRY_EXPORT, &size);

        PIMAGE_SECTION_HEADER *pHeader = new PIMAGE_SECTION_HEADER();

        // get the names address
        PULONG names = (PULONG)ImageRvaToVa(image.FileHeader, image.MappedAddress, exports->AddressOfNames, pHeader);

        for (ULONG i = 0; i < exports->NumberOfNames; i++)
        {
            // get a given name
            PSTR name = (PSTR)ImageRvaToVa(image.FileHeader, image.MappedAddress, names[i] , pHeader);

            // printf("%s\n", name); // debug info

            if (IsUnwanted(name))
            {
                name[0] = 0; // set it to an empty string
            }
        }

        UnMapAndLoad(&image); // commit & write
    }
}

BOOL IsUnwanted(PSTR name)
{
  // implement this
}

It's more some kind of obfuscation but removing names completely is more complex since it requires a full consistent rewrite of the exports section.