Browser pop-ups or file uploads can be handled using Java API Robot class

Selenium is not a tool for saving attachments etc. But  you can  solve your problem. Simple example:

    @Test

    public void downloadFromIbmlalala() throws AWTException {   

        driver = new FirefoxDriver();

        baseUrl  = "http://www.ibm.com/developerworks/apps/download/index.jsp?contentid=939418&filename=a-automating-ria-src.zip&method=http&locale=";

        driver.get(baseUrl);

        try {

        WebElement buttonFromPage = driver.findElement(By.name("verify"));

        buttonFromPage.click();

        (new Robot()).keyPress(java.awt.event.KeyEvent.VK_ENTER);

    } catch (AWTException e) {

        e.printStackTrace();

    }

    }

and attachment is saved in default location. If it’s a good idea to save attachments in automations testing? Don’t think so… But it can be done