There is a flues in EPiServer Form which all uploaded file can be indexed. To exclude uploaded file using EPiServer Form -> FileUploadElementBlock from EPiServer Find indexer you can go:

    [ModuleDependency(typeof(InitializationModule))]
    public class EPiServerFindInitialization : IInitializableModule
    {
        public void Initialize(InitializationEngine context)
        {
            ContentIndexer.Instance.Conventions.ForInstancesOf().ShouldIndex(ShouldIndexDocument);
        }

        public void Uninitialize(InitializationEngine context)
        {
        }

        bool ShouldIndexDocument(DocumentFileBase documentFileBase)
        {
            if (contentAssetHelper.Service.GetAssetOwner(documentFileBase.ContentLink) is FileUploadElementBlock)
            {
                IEnumerable result;
                ContentIndexer.Instance.TryDelete(documentFileBase, out result);

                return false;
            }

            return true;
        }

        readonly Injected contentAssetHelper;
    }