When a manual transmission grinding gears when shifting, it usually indicates a problem of a clutch that is not fully releasing. There is a problem inside the transmission that affects the meshing of all gears not just in one particular gear.
The most common reason is that the clutch is not fully releasing when the clutch pedal is depressed. It is a common knowledge that the purpose of a clutch is to disconnect the engine from the transmission so that the driver can change gears. Now if the clutch is not fully release when the pedal is depressed the gears will clash when shifting.
Repairing this kind of problem requires special skill and it will be very costly. However, if the car is still covered with warranty then nothing to worry about, just bring the car to a shop which specialized with manual transmission and ask the mechanic to check the clutch linkage.
In some cases, just a simple adjustment of the linkage will likely correct the problem. If the mechanic told you to teardown the transmission, do not agree without seeking several opinions with another mechanic.