If you are looking for regEx please use the below regex for your code.

var regEx = new RegExp("^.*\.xls[xm]?$");//reg ex for excel file

console.log(regEx.test("abc.xlsx"));// true
console.log(regEx.test("abc.xls"));//true
console.log(regEx.test("abc.xlsm"));//true
console.log(regEx.test("abc.xlst"));//false
console.log(regEx.test("abc.doc"));//false
console.log(regEx.test("SITE_ADDITION (1).xlsx"));//true

If you are only concerned about the extension use this:

function isFileValid() {
    var allowedFiles = [".xlsx", ".xls"];
    var fileUpload = document.getElementById("MainContent_fluploadData");
    window.lastUploadedFilename = fileUpload.value;
    var regex = new RegExp('\\.(' + allowedFiles.join('|') + ')$', 'i');
    if (!regex.test(fileUpload.value)) {
        alert("Please upload files having extensions: " + allowedFiles.join(', ') + " only.");
        $('#MainContent_fluploadData').val('');
        return false;
    }
}

Notes:

• you don't need to check for characters leading up to the . if you don't care about the chars in the file name, as long as you do not anchor the regex at the beginning.
• '\\.(' - if you define a string and want to have a literal backslash you need to escape it: \\
  • in other words, string definition '\\.(' becomes \.( in memory
• the second parameter to the RegExp constructor indicates case-insensitivity

If on the other hand you want to restrict the characters in the filename, use this:

function isFileValid() {
    var allowedFiles = [".xlsx", ".xls"];
    var fileUpload = document.getElementById("MainContent_fluploadData");
    window.lastUploadedFilename = fileUpload.value;
    var regex = new RegExp('^[a-z0-9\\s_\\.\\-:\\(\\)]+\\.(' + allowedFiles.join('|') + ')$', 'i');
    if (!regex.test(fileUpload.value)) {
        alert("Please upload file with only A-Z, 0-9, space, dot, dash, :, () in name, and extension: " + allowedFiles.join(', '));
        $('#MainContent_fluploadData').val('');
        return false;
    }
}

Notes:

• the regex needs to be anchored at the beginning with ^
• tweak the character class as needed for allowed chars
• on the other hand, in case you have to full path name in your filename, start the regex string with: '[\\/\\\\][a-z0-9...