I am wondering whether is there a name for a phenomenon where one has feelings of alienation or feels that body parts (limbs, internal organs, etc) do not belong to him or are not part of his body ?For example - imagine a case where someone loses an arm and is transplanted with a new one, to which he feels that it does not really belong to his body.I am looking for the name and some details about this type of psychological condition 
Is there a phenomenon where one feels alienation towards certain body parts
cognitive psychology;clinical psychology
See the relevant psychological disorders that relate to your question:Body Dysmorphic DisorderBody Integrity Identity DisorderXenomeliaXenomelia would be the most likely disorder in-line with your description. The definition is very similar to your description (Lutz and Brugger, 2012):Xenomelia is the oppressive feeling that one or more limbs of ones  body do not belong to ones self.See Sedda (2011) for a discussion around how Body integrity identity disorder may relate to Xenomelia. The author examines the possibility of BIID as being both a neurological syndrome and a psychological disorder:Recently, McGeoch and colleagues provided the first direct evidence  that the sense on incompleteness reported by BIID patients (First  2005) finds a correspondence in a dysfunctional activity of the right  parietal lobe (McGeoch et al. 2011), strongly supporting the  hypothesis that BIID in not simply a paraphilia but rather a  neurological syndrome (Blanke et al. 2009; Ramachandran and McGeoch  2007; Aoyama et al. in press). McGeoch and colleagues propose that  xenomelia, from the Greek terms foreign and limb, would describe  this new parietal lobe syndrome better than apotemnophilia or body  integrity identity disorder (McGeoch et al. 2011).See Brugger et al. (2013) as well. They examines the mind-based and brain-based considerations in understanding the nature of the Xenomelia as a disorder in itself. I've inserted an image of a Venn diagram depicting three approaches in understanding the factors that causes Xenomelia symptoms:A view of xenomelia research that integrates three approachesFrom: Brugger, P., Lenggenhager, B. & Giummarra, M.J. (2013). Xenomelia: A social neuroscience view of altered bodily self-consciousness. Frontiers in Psychology, 4, 204.ReferencesHilti, L.M., Hanggi, J., Vitacco, D.A., Kraemer, B., Palla, A., Luechinger, R.J. & Brugger, P. (2012). The desire for healthy limb amputation: structural brain correlates and clinical features of xenomelia. Brain, 136(1), 318-329.Sedda, A. (2011). Body integrity identity disorder: From a psychologicalto a neurological syndrome. Neuropsychology, 21, 334-336.Brugger, P., Lenggenhager, B. & Giummarra, M.J. (2013). Xenomelia: A social neuroscience view of altered bodily self-consciousness. Frontiers in Psychology, 4, 204.