I performed FE-SEM on hollow fibers and observed that some areas are not sputtered. Au/Pd alloy was used for sputtering. What could be the possible reason for such a scenario.
you may suffer from punctual charging effects during sputtering; especially when you sputter only for a short time and your fibers have got high resistance or are even non-conducting.
I don't think these spots are a result of absence of coating. If it were this then these areas would be charging and appear bright, or give aberrant contrast in some way. The patches are darker than the surrounding material and there are no artefacts usually associated with charge build-up due to poor conductive coat. (At least I am presuming that you are talking about the randomly distributed dark patches...)
An alternative might be that these areas are patches of an atomically lighter material on the surface such as is seen when there is some organic contamination before the coat was put on. Just a thought.
coating thickness depends on time and sputter rate; with 'sputter only for a short time' I tought on some seconds; but it is only my peronal feeling what may happen rather than real knowledge.
Just to add that sputter coating thickness will depend also on the current used. You should have a graph from the manufacturer of the coating unit that shows coat thickness against time and current for any given target material. If not, then ask for one. You can also install a thickness monitor on some coating units.
ok, I think you will have difficulty identifying any organic contaminant. One approach might be to try using a UV/ozone cleaner on its gentlest setting before coating. This might strip off any residue.