I'm using a Canon EOS 700D with a 50mm 1.8 prime lens. I normally preview the photo through the LCD screen before I click the photo. I recently noticed that my photos are under exposed when compared with the preview. It shows a brighter image for a small time when I halfway click the button, but the actual image is under exposed. I tried clearing all the settings, but that didn't work. This only happens in Manual mode. Does anyone know why this happening?
You probably use a small aperture. When autofocus does its work, it usually does it with wide open aperture. That's why you get a brighter image for a small time. It says nothing about the brightness of the final image. This may be different when using phased-based autofocus and contrast-based autofocus, but this depends on what the camera does.
Some cameras might have an option for a "framing" vs "preview" display either in live view or when using a through-the-lens optical viewfinder: in that case "framing" gives full brightness but less depth of field than the actual photograph may have, while "preview" corresponds in brightness and depth of field to the final result.
Looking in the manual, it would appear that you have a depth of field preview button to the upper right of the lens mount. Pressing that should reduce the brightness to the actual brightness that is going to end up in the photograph, at least when using the optical viewfinder.
You simply need to adjust you LCD brightness. Turn it down a bit and use the histogram to determine exposure instead of relying on the LCD. The LCD image is competing with ambient light for your eyes attention. Your eyes can cause the problem by not adjusting for the LCD properly. Use the histogram.